I'm having trouble with using bows. How do I equip one with arrows? When I equip one to my rogue it says 'no arrows are equipped' even though I have arrows in my inventory.

Also, do arrows become more common later in the game? And can they be collected and reused like throwing knifes?

Put the arrows in the other weapon slot. Arrows can be reused.

Also, answering the other two questions, yes. I have 27 arrows and 20 bolts, and rarely use them all in a single combat. You can just grab them afterwards. However, they lose the enchantment they may have when you shoot them.