Regardless of the state of the skeletons after Skeleton Crew was cast, they cannot be animated again only if they were destroyed, otherwise they return to their original state as corpses. Corpses are valid targets to Animate Dead and Create Undead.
The description of Skeleton Crew does not state that they are destroyed upon the end of the spell. And unlike animate/create undead, which are permanent, skeleton crew has a duration.
However, you cannot create zombies with Animate Dead, only skeletons, as their flesh melts away into fog.
A skeletal crew member can only be created from a mostly intact humanoid corpse. The corpse must have bones. When you cast this spell, any flesh left on the corpses melts away into fog.
From a rules as written perspective, note also that only Animate Dead has the clause about not reanimating the targets again. Which means that Skeleton Crew could be re-cast over and over again on the same targets, even if they were destroyed.
A destroyed skeleton or zombie can't be animated again.
Create Undead, however, simply says that it's a more potent spell than Animate Dead, so any undead created using it are fair game, even Ghouls or Huecuvas.
A necromancer that is worried about the lack of corpses (the world mysteriously has few cemeteries), should consider raising them as Bloody Skeletons instead.