That's not really the problem since late-game is not supposed to be played alone and you can still use AoE abilityes or skillshots on her if you have a red trinket (or are lucky enough). The problem with vayne is that she gets a lot of free damage off even when you the counterplay right. You just can't negate her damage, there's no way around it, she will ALWAYS proc silver bolts at least once during a trade and chunk you too hard for you to actually catch up with her, your only bet is to outdamage her and, unles you're a hyper-bursty champ or a hypercarry yourself, you just can't hope for it, especially counting that she does a lot of true damage.
She's balanced overall, maybe she gets her powerspike too soon, or maybe silver bolts should just be a straight up on-hit instead of a 3 hit since that would actually be more fair on her actual kit imho so she does need to be looked at a bit imho but really, the stealth is the last of her problems imho.