Some blocks can't be removed from the map, usually the static ones (compiled with the map).
The ones that we are able to remove through plugins / .lmp files / stripper is the entities that the server can read (usually a env_player_block)
You can check most of them using "r_drawclipbrushes" in console (local server).
https://developer.valvesoftware.com/...rawclipbrushes
You can remove it only if you open the map in hammer delete it and them compile back, but it will generate a new version of the map and everyone will have to download it (like a custom map), which is not a nice solution.
What I have seen is some servers using a portal entity (don't remember the name) that allow you to "teleport" to some specific places, so sometimes you can't reach a place cause there is an invisible wall, but from the there side of the wall you are able to move.