After 10 years of a distinct Scottish presence at the Venice Biennale, it seems there is now an appetite for a kind of reckoning.

Since 2003, when the Zenomap show launched Scottish contemporary art's contribution to this often bewilderingly big and essentially ungraspable festival, more than 40 artists have displayed their work on a Scottish stage. Reputations have been made and others secured.

Beside the estimable work of a generation of artists, a generation of gallerists and curators have engaged with the process. The tireless efforts of the curators and assistants who, over the years, have worked within strictly delineated budgets from Creative Scotland, the Scottish Arts Council, the British Council and National Galleries have, show by show, contributed to a striking Scottish vision which one cannot imagine removed from Venice's kaleidoscopic survey of today's art.

Any future idea of non-participation in the "coming together of the world", as Fiona Hyslop, the Culture Secretary, put it, would be a mistake. The cost, around £500,000 from a few different funders, for a six-month show, does not appear exorbitant. "The quintessence of the Biennale is participation," the president of the festival, Paolo Baratta, said this week.

But how to "participate" in this festival – that is the question that some minds in the Scottish art scene are ruminating on. There is now a train of thought among those who have backed the scheme over the last decade, that some kind of survey or recalibration should be considered.

Is, for example, Scotland + Venice engaging enough with (and to) the wider contemporary art scene in Scotland? Will the (belated?) national acknowledgement that is the Generation show, which will be staged across Scotland next year, of the country's (and Glasgow's) contemporary art scene feed into the next show?

Who else, or how else, could a future Venice show be staged? Is it time to return, after this year's three-artist show, to a solo exhibition? Is the current venue, which has been used three times, right any more? And what will Scotland + Venice mean, or look like, if the nation votes 'Yes' next year?

These questions, one senses from a week in and around the Biennale, are being asked and will be asked more publicly in the coming year.

Certainly although the next Scottish show might be (conceivably) radically different in form and function from the last five, 2013's version is reassuringly rich and strong. The Scotland + Venice show, somewhat off the beaten tourist track at the neat and domestic Palazzo Pisani near the Rialto Bridge, is strong and complex, dense and time-consuming.

Duncan Campbell's examination in a nearly hour-long film – using dance, animation, essayist film clips, titling and voiceover – of commodity, exchange, capitalistic equations and, quite tenderly, communications of love's own currencies, required concentration and comprehension. Even two sittings does not seem to do it justice. His previous films centred on people – Bernadette Devlin, for example – with their own narratives and histories, but here Campbell tackles abstract ideas of exchange and value. It makes for a sometimes confounding but challenging film.

Corin Sworn's film is more fluid and formerly attractive, but it also, in her take on her father's sociological travels and investigations in a Peruvian village battling for its land, shares a unintentional parallel with Campbell's musings of exchange and market. The use of slides and snaps, not always entirely accurate in their capturing of memory, is deft and beautiful.

A little like microscope slides, or perhaps petri dishes, are Hayley Tompkins's alluring dropped paint works which could almost be scientific distillations of the clear-cut images she has gleaned from the internet, and which lie on the floor beside them.

Overall, unlike the Karla Black show in 2011, which blazed on the viewer's eye from the first moment you completed your ascension of the Palazzo's stairs, or Martin Boyce's ghostly sculptural show in 2009, Scotland + Venice this year is not strikingly immediate – but it repays the time invested in it.

So too does Jeremy Deller's UK Pavilion, which initially strikes you as fragmented but then, over time, becomes rather wonderful. One wonders if there has been an angrier or more left-wing show at the venerable neo-classical pavilion. Deller has strong links to Scotland: his gallery representation is Glasgow's Modern Institute, and he visited prisoners in HMP Shotts for part of the show. He, of course, launched his wonderful bouncy Stonehenge – Sacrilege – in Glasgow.

Here, the video of a Range Rover being crushed – part of the "daydreams of destruction" which characterise the show – was shot in a Scottish breakers yard. The show's large murals of righteous destruction – of the tax haven of St Helier, of Roman Abramovich's ginormous if sleek yacht (which was moored to the lagoon front near the Giardini gardens in 2011, causing much discomfort), of someone's Range Rover by a gigantic Hen Harrier – are vengeance fantasies. The heroes of the show – David Bowie and William Morris, A Guy Called Gerald and (beautifully) Vaughan Williams – have personal or artistic links to the English Magic from which the show is entitled.

Hidden people, deceptive illusions and dark trickery preoccupy Deller. He says in the show's booklet: "Despite the popularity of contemporary art in the UK, I think some people view it as a secret society, to which you're not welcome. The art market at the top end doesn't help: ultimately it has an alienating effect on the public."

Not too much of the work on display in the national shows at the Giardini and Arsenale, or the many collateral events, has that effect however. It is invidious to try and lay a blanket theme over the entire, vast festival, but the real and the unreal seem to be the concepts most taken to task.

So in Ai Weiwei's show Disposition where, in six great metal containers, he presents the very real: artistic renderings, in immaculate sculpture, of his 81 days in imprisonment in 2011. Seen only through square portholes, models of Weiwei eat, sleep, shower and defecate under the eyes of watchful guards. The six containers, like cells or beached submarines, are placed within a beautiful Venetian church, Sant' Antonin in Castello. It is both moving and chilling.

The Vatican's contribution, a first for the Holy See, could be a secular show: it takes the theme of Genesis and bends it in different ways. The black and white photographs of Czech photographer Josef Koudelka show a world destroyed, by war or famine or worse. Chara Boyle, who has filled the modest Canadian pavilion (hiding between UK and France, perhaps aptly) into a mythic cave, filled with statuettes carrying globes and a grotesque panorama which is suddenly enlightened by lights and pictures.

In the US's superb pavilion, Sarah Sze has invested the rooms with brain-manglingly dense installations that could be scientific or craft work stations, or could be useless. Her big, created boulders are scattered on surfaces that have rumbled into the real world, too, placed in different positions throughout the Castello area.

Most rewarding of all is Il Palazzo Enciclopedico (The Encyclopedic Palace), the vast show which fills what used to the Italian Pavilion.

Taking in fantasy and imagination and "outsider artists" (that is, untrained or maybe slightly unhinged artists), it is a wonderful fractured landscape of dreams and nightmares, performance art and pure painting.

Steve McQueen and Cathy Wilkes, with a moving diorama, are here, as is Carl Gustav Jung's personal Red Book. Replete with beautifully coloured visions, like William Blake via Rothko, it is central to the pavilion's concept, but the show, expertly curated by Massimiliano Gioni, is full of wonders. The throbbing proto-minimalism of Hilma af Klint, a Swedish visionary, lingers long in the mind, as do Pawel Althamer's liquifying but perfect-faced figures, which fill a haunting room in the Arsenale.

La Biennale di Venezia runs from June 1 to November 24.