Yes, but the thing is, EV bonuses are applied at level up. Since you can't level up anymore, your EVs won't ever get a chance to go up, so it's pointless.
In the older games (RBY, GSC, maybe RSE/FRLG, not sure), you could simply deposit the Pokemon into the PC and withdraw it, and the bonuses would be applied, but not in Gen 4 up.
To be more precise, you technically can effectively EV train a Pokemon at level 100, but only through the use of vitamins (which have a limit, and can't max out an EV), and not through fighting wild Pokemon. This is because you gain the EVs at the same time as gaining experience points, and since a level 100 doesn't earn exp, it doesn't earn EVs.