Maybe. What I do is rare candy them up to ~50, then give them vitamins (vitamins increase the EV of a certain stat by ten up to 100 EVs), then train them on pokemon that have 2 EVs of the stat I want, along with having pokerus and a power item. Goes by faster that way.
And basically, yeah, because the EVs will be screwed up, unless you want to use all those EV reducing berries (Hondew and such, the ones that increase happiness) and re-train those pokemon, the team you beat the Elite 4 with won't be optimized. Good for sentimental value though. EV training doesn't mean too much in the story mode, but its a big difference in competitive battles. In friendly battles they should do just fine, but if you're going up against someone who knows their shit, you might lose. Esp. since your pokemon will probably have lots of HMs that are otherwise worthless.