You have a level file that contains more information than just geometry+actions (wmb).
Create a custom file format (reference to wmb or something) that also contains path information, so path nodes, cover points and so on.
Then load the path information in your game into a fast data structure (quadtree for shooter levels eg) and search suitable cover points as soon as you need them from your precomputed storage (level format).
If you need dynamic cover points that move with entities, just search them as well but don't treat them equally.