First, the level cap is 100, not 50.
Second, Wi-Fi battles only scale a Pokemon to Lv.50 to keep the playing field between players even. This has no effect on the ability to train the Pokemon outside of it, and EV's have effect at every level. (At Lv.50, you get +1 for every 8 EVs)
Third, the "box trick". When you put a Pokemon in the PC, its actual stat values (HP/Attack/Defense/etc.) are discarded. When you view it in the box or take it back out, the game silently recalculates those values from scratch (thus reflecting any new changes in EVs).
Fourth, as of G5 stats are reportedly recalculated after every battle, instantly reflecting any noticeable changes to the individual's EV's. In prior generations, a Pokemon at Lv.100 did not gain any more EV's because they did not gain any experience points (though items and the box trick still works).