Absinthe,
It seems to me that reducing a 6” pipe to four 3” pipes and then closing three of the four 3” lines with blast gates would, for sure seems intuitively more efficient, since air is only being sucked through the one 3” pipe and no suction is wasted. But a problem could arise back in the main 6” line, where air flow must be kept moving at a velocity greater than 3500 feet per minute. I suspect that a single 3” line through which air is pulled could reduce the velocity of air in the 6” line and allow debris to settle in the pipe. Leaving all four 3” lines open would, I suspect, ensure enough air is pulled through the main 6” line to keep debris from settling out.
Another aspect of reduced air flow in the cyclone, which I would think could occur if only one 3” pipe is used to collect dust would be related to separation of course and fine debris. As I understand cyclones, separation depends on the speed imparted to dust as it travels through the cyclone. The greater the velocity of the particle, the more likely it will be cast into the dust collection bin and remain out of the filter stack. If in fact that 3” single open pipe reduces the velocity of the particles, then more debris could end up in the filters.
My arguments could be affirmed or refuted with some measurements and calculations, but I am just not up to that task.