Jones - the pump in the inflow chamber is used to supply the skimmer.
I think what you are trying to say is put holes near the top of the middle baffle in the bubble traps? That would defeat the purpose of the bubble traps. The design is to force the water (and bubbles) into a thin layer at the surface, giving the microbubbles time to pop before the flow reaches the return pump so these bubbles are not conveyed to the display tank.
Most SW tanks don't use mechanical filtration. Any detritus in the tank is usually taken care of by microorganisms, clean-up crew, and other small sandbed or liverock-dwelling creatures. With mech pads, the stuff gets trapped where these organisms cannot consume it, so it breaks down and contributes to the nitrate level, which in a reef tank, we strive for zero nitrates so this is problematic.
masterkaw - your second drawing is the design i'm using now. I'm using a 20 long tank, and have approx 850gph going through it. I get a lot of microbubbles, but you're right, you can adjust the flow through the fuge. With a larger tank you may have better luck with the design than I have.