Despite a wealth of sporting talent, success as a separate Scottish Olympics team would not be simple and would take time because athletes would have to get accustomed to a new training environment and new coaches, the six-time Olympic champion said.
Sir Chris said he has decided what he will be voting for but refused to be drawn on the independence debate.
Speaking to BBC Radio 5 Live, he said he has been indirectly approached by both sides but does not want to get involved in a "hornet's nest".
He said: "I don't want to get drawn into it. I've said numerous times how proud I am to be Scottish and how proud I have been to compete for Britain too, and I don't think these two things necessarily have to be mutually exclusive."
Asked if he knows what he will vote for, Hoy said: "I suppose I do, yeah."
On the prospect of having a separate Olympics team in an independent Scotland, he said: "You look at the results of the Scottish athletes over the years and we have had some fantastic athletes and some fantastic results.
"But it would not be quite as simple as just saying, 'there is a Scottish athlete, they have won a gold medal, therefore that's a medal for Scotland'. Most of the athletes have had to move to facilities which are often out-with Scotland.
"I had to move down to Manchester because there was not an indoor facility in Scotland. I went to Manchester, trained with the British team and benefited from that.
"The first thing you have to do if you're really serious about it is you have to provide the facilities and the coaching infrastructure.
"In Scotland we have the Institute of Sport and SportScotland there to try and give support to the athletes. There is support but it is not quite as simple as saying 'we had x number of medalists from these Games, therefore that will translate into the same medals next time'.
"It will take time. It will weaken the British team obviously if Scotland went separately, and it would be harder for the Scottish athletes initially to establish themselves in a new training environment, with new coaches, with a different environment altogether.
"It's not to say it's impossible but it would just be a different challenge."