I've seen this problem first hand myself, but I believe its to do with the base game rather than the mod itself. it happens when you delete a ship variant while other ships are still configured in said variant. So for example, if say, 2 atlases are saved as the variant "super cargo ship", then you delete the ship variant, the game crashes as it tries to reconcile the fact that the ships that are saved as the "super cargo ship" variant, a variant that no longer exists (because you just deleted it).
to get around this bug, get every ship that is saved as the variant you are trying to delete, and load a different variant for them. once that is done, then you SHOULD be able to delete the variant without crashing.