I dunno about San Andreas yet, but I have a 100% complete save file for Vice City that I did with cheats, and same goes for GTA3. (GTA3 on both PS2 and XBox, VC on XBox) You just had to be careful WHICH cheats you used. In Vice City, for example, I used the health, armor, weapons, and arrest-rating codes more times than you can shake a chainsaw at. I also activated several codes for spawned vehicles, including tanks, hearses, racecars, etc. as well as costume cheats. I did, however, stay away from any cheat that changed game mechanics or universal effects - like angry pedestrians or vehicles driving on water. Jeez, I even saved a black PCJ from the "all-black vehicles code" in my garage and then rebooted - the cheat turned off, and I kept the slick black sportbike. And when I got to the end of the game, I saw 99% - I thought the old myth was true.
But when I compared a 100% complete checklist with my stats screen, I found one minor difference: the shooting-gallery mission. That one forgettable mission was all I needed at that point - and now I have the 100% save file to prove that the myth is busted.
Each of my friends that said they had activated cheats and therefore couldn't get 99% on Vice City (both PS2 and XBox) all complained. But, one by one, I helped each one go through the checklist - and each time, it turned out to be a missing hidden package, side mission, rampage, or unique jump, and most often, it was that Shooting Gallery mission at the guns and ammo store on the second island.
The only major difference I ever saw with my cheated file was my mobster rating - instead of having a Capo or Don rating, I'd end up with Lunkhead or whatever it was and a negative criminal rating. That's okay - a few Brown Thunder missions always managed to get that rating back up, though.
I understand that San Andreas has a few ways to lock out cheaters, though - makes me wonder why Rockstar bothered to keep them in. I don't know whether it means never achieving 100% or not, though - but if it's anything like Vice City and GTA3, then you'd be better off checking your stat screen, line by line, and comparing it to a 100% checklist than simply assuming it's your health codes that did it.
-Darquewing