I don't know of any I/O monitors, but I believe that USB 2.0 is more heavily "processor-dependent" than FireWire (meaning FireWire puts less overhead on the processor and more data handling is done on the FireWire controller chip, vs. USB which uses more processor cycles to operate).
Modern hard drives have a theoretical throughput up in the 40-70MB/sec range, but you'll hardly see that in the "real world" unless you've got a RAID setup with multiple drives. Most 7200RPM ATA/SATA drives will top out around 30MB/sec, and that's being generous.
If speed is your main concern, then I can see why you'd want the best setup for your USB hard drives and to maximize usage of different USB chips, but I really don't think you're going to notice much slowdown implementing what you've described (two USB hard drives on a single USB controller chip).
It seems from the developer's notes over at Apple that the Mac mini has one USB controller chip that controls multiple USB ports:
http://developer.apple.com/documenta...section_2.html
However, that documentation may be out-of-date for the newer Intel-based minis. I wouldn't think that Apple would throw in more USB controller chips in the move from PowerPC to Intel, but they may have.
If you have some spare USB hard drives around to test with, you can always use XBench to measure throughput of drives, available here:
http://xbench.com/