Since two people have talked to me about it in the past two weeks, I'd like to destroy the myth of the overlapping brushes.
While I do agree that overlapping will make HLVIS take longer (needs to make extra face splitting calculations) it will not affect HLRAD since HLRAD uses the information that has been decided in the previous process. When the RAD process occurs, those extra bits of brush have already been discarded and have absolutely no effect in the process.
In the following screenshots, I have made a version where there is no overlapping, and another one in which the pillars go through both floor and ceiling. As you can see by the r_speeds and gl_wireframe, they are absolutely the same. Their differences have been solved in HLBSP and HLVIS.
No overlappingOverlapping pillarsConclusion. If you want a tidy compile, avoid overlapping brushes. If you are worrying about ingame frames per second, this has nothing to do with it.
Edit: there's another kind of overlap consisting of simultaneous brush faces occupying the same place in the map. This should of course be avoided!