Reading and writing to USB in a non-critical loop would definitely lower determinism. It will probably still be more deterministic than Windows, but it isn't optimal. If that USB drive is a shared resource, then you also run the risk of a
priority inversion.
How fast USB is polled depends on the particular system. I usually pull out the number 1000 because I think that's the theoretical limit of the standard. It would make sense for the USB drive to be polled less frequently when not actively transferring data, but I'm not familiar the USB standard to that degree.
These KBs, which should probably be merged, talk about jitter caused by USB and how to disable USB.
http://digital.ni.com/public.nsf/websearch/3cf9e0de9940b11e862568d200800739
http://digital.ni.com/public.nsf/allkb/9171AF026183A6EB862571AB00820757?OpenDocument
Trey B | Applications Engineering | National Instruments