Yes. Bungie has claimed that all weapons will feature skill trees to customize weapons. I personally believe that this feature will behave in accordance to the rarity of a weapon, however. For example, a common gun will probably have an inferior skill tree compared to that of a superior or exotic weapon, in both perks and size. So, a good weapon could be used and upgraded for a good time, then you can move on to another, better weapon to invest in, rather than sifting through piles of guns looking for minimal improvements.