After completing the main missions, do cheats affect side missions and block getting 100%?
Yes, the in game cheats can end up stuck on their activated state prevent the completion of the 100% of the game.
Some cheats like Wanted Up and Wanted Down can lock your game to Never Wanted, so the gold on some missions like Breach of Contract become impossible. The same goes with Explosive Melee getting stuck and ending up with Closing the Deal being impossible.
Other ones like Slow Motion and Slow Motion Aim can prevent your game from triggering certain animations because they are messing with the internal game timer.
I can confirm that this happens on versions PS3 1.35, 1.36 and PC 1.44, 1.45, 1.46, 1.47, 1.48.