Padded shorts / liners / tights etc are designed to wick moisture away from the body (as well as providing additional comfort, not having seams in all the wrong places and so on) and are therefore - IMHO - more hygienic than cotton knickers for vaginal discharge. And I can also report that they cope surprisingly well with one of those 'not making to a toilet in time' incidents if you're on your period. *sigh*
If I'm popping into town, I don't normally bother wearing padded liners but always wear them or lycra for rides over 20 miles, which seems to be my comfort threshold.