Question

If I have a level 100 Pokemon on X and Y and I use the reset bag on it, will it have any negative effects?

Answer 1

No, it won't have any negative effects, but of course it will reset the EV's in all of your Stat's to 0.

If you want to get rid of some EV's from your Stat's and not all of them, you could use EV Reducing Berries instead.

If you don't care about any of the EV's your Pokémon has at all and you just want to reset it's EV's to 0, then the Reset Bag is obviously the best way to go about it, as you can still EV Training Pokémon when they have reached Level 100.

Answer 2

A Reset Bag resets all EVs of a Pokémon, so if your Pokémon has EV trained, it will remove all EVs and you will need EV training all over again.
If you EV training in a stat you didn't wanted, Reset Bag is useful!
I don't see any negative effects apart of deleting all EVs.

Answer 3

Except that it will reset all your EVs (which is probably what you want), it does not have any negative affects as you can still re-EV train though the super training and wild Pokemon.