Is it smart to cut (with like a bolt cutter or dremel) or file (hand held) shafts/metal that are already on the bot? my fear is that they get bent

I would never recommend cutting or filing any metal that is attached to the robot. The metal shavings alone could get into motor ports and mess stuff up, but yeah shafts bending could also be a problem.

So overall unless your at a competition and literally have no time because you just failed inspection and now have to cut your bot in half to fit in size, I would take it apart and cut everything separately