I don’t bother with a good fast USB hub - using the QSI 683. With low bandwidth USB ports (like those on netbooks), I have seen problems in the past with download speeds causing striping. I do pause guiding during autofocus but in truth, I have not compared it with and without. I’m using PHD2 and a Lodestar BTW, rather than the QSI ST4 port.
I guess the autoguider could affect the quality of your focus results, although I’ve never experienced that, and the change in focus could cause your OAG to lose its star I you are using an OAG… and I’ve never experienced that either, even though I use an OAG.
So now, I don,t worry about it. One less chance for something to wrong when stopping and starting the autoguider… But if I started having trouble, then I would think about pausing again.
As an aside, I had a brief problem with a recent beta (I posted about it) that has since been resolved… but when trying to resolve it, I softened many of my criteria… pause during guiding, reduced amount of dithering, reduced settling time, increased settling tolerance… none of these had a negative impact that I can see on subs, but it has lead to less time “waiting” between frames.