Yes I know it's lazy but I leave my pertex shells in their little bags between trips (unless they're wet). Will this reduce their windproofness/durability? Should I bother to unpack and hang them up instead? Thx.
Does indeed sound like the height of laziness 
I got into the habit, a very long time ago, of completely emptying my bag post-trip after finding a couple of little passengers (ticks)*. Stuff gets taken out, given a shake and a visual check. Takes 5 minutes, tops.
You could always re-pack again straightaway.
*Not to mention, on occasion, errant bits of food, un-noticed spilages etc.
Trouble no one about their religion;
respect others in their view and demand that they respect yours.
~Chief Tecumseh~