Brushes and Lag Question
If you are worried that the brush count is too high and it cuts performance greatly, you can always use culling techniques such as area portals, fog, or good placing of hints. Also the design of the chambers itself will improve performance if you think in terms of visibility.
If you are making a large single player campaign, split the levels up and connect them using a transition. If it is coop, you should only have one chamber set per map, the disassemblers should take you to the next chamber set.
By eliminated, I mean it should be merged with adjacent brushes. No need to delete them.
The rule of thumb is that you should cut brushes only if you need to modify its shape or change its texture. Otherwise, I wouldn't go about clipping brushes all over your map with no intention of modifying them.
Doing so would increase the BSP filesize unnecessarily, and it would impair performance.
Again, everything we do must have a logical reason behind it.