CSG subtract is bad because it may create uncessary braushes (negatively affecting r_speeds), it can create hidden texture faces (slows down compiles), it can cause errors within the map that don't become evident until you compile (some very serious and hard to fix), it can error itself and cause splits to surronding burshes (negatively and potentially drastically affecting r_speeds), it can...etc...etc.
It is evil and I don't know any experienced mappers that use it except for some brave souls, in very controled situations where it can not affect the map as a whole (like prefab construction) and they are always aware of the problems it can cause and prepare to repair.
There is nothing you can do with CSG subtract, that you can't do by creating and shaping your own brushes. But when you do it, you won't cause any of the problems that CSG subtract can.
So heed my warning, don't use it.