Most definitely it changes the amino acid profile of a food, and at the extreme end of things it may produce toxic/carcinogenic molecules. But the Maillard reaction occurs without cooking (eg long term storage of foods) and also occurs in your body, especially when fructose consumption is high, so NOT cooking your foods does not necessarily prevent their formation.
As bodybuilders I'd say you don't need to worry too much about it. Lysine is the main AA that's affected, but almost all BBs get more than enough lysine anyway. The only people that might have to worry about this conversion are folks that are already taking in marginal protein and marginal lysine to begin with.