ECS on its own doesn't always help - it's not a magic bullet for every situation: sometimes you need to use spatially-aware data structures / acceleration structures for those type of "queries", and vanilla ECS (i.e. similar to a DB in terms of queries) doesn't always help you in these type of situations.

And how many games actually do that?

Also, if you really want, with Godot you can bypass the scene node system and also just use C++.