For instance, Vayne's Silver Bolts don't have real "counterplay"
Vayne's silver bolts have counterplay - counter-building just isn't part of it.
I feel like you're confusing lacking 1 counter-stratagy as lacking counterplay.
What are things that SHOULD NOT have counterplay?
Everything should have counterplay.
The entire idea behind counterplay is that mechanics should be as engaging to play against as they are to use.
Riot seems to use this to allow options when dealing with a certain mechanic.
Sometimes you can dodge a play, sometimes you can disable a play with CC, sometimes you can duck in brush/fog of war/stealth to break someone's play pattern, sometimes you can back up against terrain, sometimes you can stay away from terrain, sometimes you can use minions as cover, sometimes you want to keep your distance from minions, sometimes you can just tank a skill to the face and plan on doing so because you itemized to be beefy...
Important thing with choices is this though: if the same choice works 100% of the time, you don't really have meaningful choices.
Dynamic decision making is at it's best when doing the same thing every time will be wrong some of those times, forcing players to adapt to the situation, identify ~3 paths of action in dealing with a problem, and picking one of those.
In the case of Silver Bolts: you simply can't counterbuild that skill as a viable counter.