That's an interesting point, and something I believe that can be seen especially with Gold skeletons, as it takes a number of shots with the flintlock or EoR, but only one point-blank shot with the blunderbuss.
I don't know if that's because if you are at range you are safer, and thus they are trying to entice pirates to enter into close quarters combat or what. As it is, none of the enemies have a health bar, so we cannot really see what damage is being dealt by each shot.
I guess I personally don't have a problem with it. Playing D&D you get used to different weapons effecting different creatures differently. There are different types of skeletons as well, even disregarding "special" types (like gold, plant, shadow), there are skeletons with pink bandanas, all-white skeletons, and skeletons with little bits of grey on them. Pink bandana skeletons seem to be the toughest of the "normal" skeletons, with the "bits of grey" being the second hardest, and "all-white" being the easiest.
Am I right? Are there these types of skeletons or am I seeing something? Anyone know what the difference is?
As for rebalancing: I guess everything seems fine to me, so I don't know if that's necessary. I think they tweak certain things behind the scenes every so often anyway.