So they do not block mouse clicks.
It was changed a couple patches ago, and it is super annoying. Quest ends say, your trying to loot, but the chest comes up in the middle of the screen, and so do all the pop up messages - right over top the chest you are trying to loot, or your inventory, or whatever - like trying to find a particular potion or weapon you didnt have hotbar'ed and are getting attacked while looking for it, and something in the quest pops up a message right over your inventory and blocks you from getting it until you have to fiddle around moving screens around just to be able to click around it.
They are mostly translucent, and you used to be able to just click through them to whatever was behind it no problems. It changed, and while not game breaking sure, it is crazy annoying when it happens.