Actually it won't, you can still get 100% using cheats.
For one, it worked for me personally in Vice City. I used the health cheat a lot, and I got 100%.
And also, don't remember the site name, but the guy has pictures of his file, because he has a bunch of maps showing different things since he's gotten 100% already...and under his stats, Use Cheats says, yes....so evidently cheats don't stop you from getting 100%