I have 9 bikes of different manufactures and all of them have these issues with 'clunks' and shifting to a degree (some worse than others). Sometimes: upshifting to 2nd at a stop prior to engaging 1st gear, eases the situation.
I've pressured washed my factory bags with a garden hose and never noticed any water inside afterwards; but if really concerned, fall back on the old fashion/time tested remedy of plastic trash bags for piece of mind.