I think third edition gave them something like DR 5/bludgeoning, and I think zombies had DR 5/slashing to kind of balance that out. Second edition didn't have a codified language for that sort of thing, but gave an ad hoc half damage to skeletons from edged or piercing weapons.
As for why it shows up in 5E, as it does, my best guess is just design error. Since the monsters were translated over a period of time, and skeletons were probably one of the first to go through the process, the designer involved probably thought that a lot of things were going to end up with resistances and vulnerabilities; and it simply didn't turn out to be the case. Another example of this "early installment weirdness" is probably how lycanthropes are immune to non-silver or non-magical weapons, where almost everything else in the book just has resistance.
If I wanted to be more generous, then I might say that skeletons and lycanthropes are included as they are as an intentional guide for DMs to design their own monsters. By having these traits, it kind of tells the DM that it's okay to include those sorts of things for their own monsters.
I think it is more of a fact skeletons have traditionally been weaker to bludgeoning, and making them resistant to the other types of damage raised their CR beyond the desired level.
As for werewolves, I think since they removed damage reduction as a standard concept, a DR 10/silver translates to immunity to non-silver weapons much more than resistance. I mean comparatively a level 5 fighter might be hitting for 2d6+4 damage.. or 1 damage on average, vs if they made it resistance, they would be hitting for 5 damage on average, immunity is far closer than resistance, And fits the mythology of werewolves being nigh unstoppable without silver weapons.