Possibly. I didn't mean to be, I was just being honest. I will not read over 3000 characters without a single line break, that's unnecessarily exhausting. Thanks for inserting some.
Now it's at least somewhat readable and the only problem is the abundance of ship lingo I don't fully understand, which I suppose naturally comes with such a project, and a failure to get to the point.
Am I correct in summarizing your problem thus: "I have beams going through multiple rooms, should I cut them at the walls so parts in other rooms need not be drawn or should I use a single brush to keep the brush count low?"
If so, that's somewhat hard to tell but probably won't matter much either way in the end, proper usage of detail and structural brushes is much more important. Focus on getting that right and maybe upload your map to let some experienced mappers take a look and give you hints.
To debug vis work, you can compile with -saveprt and use the Radiant's prtview plugin to take a look at the generated portals.