Depends on the collector...in regards to value. If the damage is severe enough it definitely warrants a diminished value. I display in box and personally would prefer non-crushed boxes. Slight damage is pretty hard to avoid. Like a small crease here and there I would probably be ok with depending on the specific location of the damage. If the damage is isolated to the back of the box or the bottom of the box I'd more than likely be just fine.
Its hard to find pristine boxes anymore though. Regardless if you are buying in store or online. I mean B and N and HT are both notorious for having less than perfect boxes in store. Not to mention HT is known for slapping huge % off stickers on the cardboard front of sale pop boxes.
Your best bet to avoid box damage is to visit stores in person and hand pick stuff

. I do feel for you though, seeing that these places are selling collectibles they should all know how to properly secure the items before shipment.
However, some good online sites to order from IN MY EXPERIENCE are: ABCTOY4ME.com, Plunderrun.com, Entertainmentearth.com, geminicollectibles.net and Popcultcha.com<---- my experience with these guys was ok due to the fact that I was able to message them and ask for triple bubble wrap.