The Digi002 and Mbox have their own internal clock reference when Pro Tools is set to "Internal" sync mode. In addition, they have a PLL which slaves to an external digital clock when using S/PDIF or ADAT clock sources. As a result, the host computer does not play a roll in the clocking of the A/D and D/A converters.
Therefore, the USB or 1394 (FireWire) connections will not influence the sound/quality of the audio in this respect.
However, the communication and data flow between the host computer and Mbox/Digi002 is still "time-critical" in the sense that there are buffers on the host side which must be filled/emptied at a certain rate, or else they'll underflow/overflow. This is the tricky part of writing the driver & audio engine code.
But again, the buffering considerations do not impact the A/D/A clocking. The buffering just impacts the amount of input-to-output latency in the system (small buffers have lower latency). Very similar buffering issues exist with PCI cards, too.