-even with her silver bolts most of her damage is still physical, frozen heart and randuin's are especially effective because she does all of her damage through auto attacks.
-yes she's a hyper carry but her laning phase is terrible. match her up against a lane bully like leona, graves, or blitzcrank. or have the support poke her out of lane.
-if she gets behind during the laning phase than it's very unlikely for her to make a comeback because of her horrible wave clear. Vayne has the worst wave clear of any adc. if vayne is behind she has two choices, farm minion waves for eternity, or try to get kills in teamfights. to counter the first plan a gank when vayne pushes the lane past a kill bush. to counter the second just focus her down when she comes in range.
-this point needs to be said again. Vayne has horrible waveclear, because of this Vayne does not do well in seige scenarios, on either side. she doesn't have the wave clear to defend on a siege and her low range puts her in alot of danger if she wants to dive the inhibitor turret where she can't stealth if things turn bad. this puts her at odds with her hypercarry identity. the main way to get to lategame is to have a strong defense so you can stave off any enemy sieges, but if your mid isn't a waveclear god like ziggs or xerath then you better hope they don't start sieging your towers.
-while she does have a auto attack range of 550 (slightly above average) for an adc her effective range* is low. This puts her in alot of danger. if she's behind and trying to farm champions in team fights focus her down cause she's still very squashy, and if she can hit you then it's very likely you can hit her.
there is no need to balance vayne. she's where riot wants her to be: a difficult but awesome marksmen that scales hard but loses to certain lane matchups.
*effective range = the range a character needs to be in order to do damage. all other adcs have spells that they can use from a safe distance when the enemy is not in auto attack range. some adcs have high effective range caitlyn, kog'maw, jinx. vayne has the lowest effective range because in order to do anything she needs to be in auto attack range. graves, urgot, quinn, siver, all have abilities that extend their effective range.