Yes it is true that pannier hooks tend to snag clothes when used as shoulder bags. One of the better solutions I have seen to solve that problem, is Ortlieb's QL3 system that put the hooks on the rack, not on the pannier. No personal experience with QL3 though. The Ortlieb Office Bag can be had with QL3.

Carrying the pannier with the hooks facing away is of course doable too, but for me at least, it just feels so unconsciously wrong to wear a shoulder bag like the Office Bag the wrong side out, that I often forget to do it.