Are These Skills Still in the Game Data?

[Sove92]

They are also there because some NPCs use those abilities and taking them out completely would force them to redo many events, cutscenes, etc.

Skills used by NPCs are separate skills entirely. They may share a name and animation, but usually the effect is at least slightly different. And obviously they don't have the same potencies nor do they have combos. There are some NPC skills that have the exact same effect, but it's still not the same skill players have or once had.

[Recon1o6]

they are still in the game. Modders frequently make mods to restore these old skills over uglier modern ones. For example power slash over soul eater

[Thurmnmurmn]

Fun way for longer time players to see old abilities. Remove your jobs stones and you'll still have your old class bars from back when you lvled with all the greyed out spells.
Unless you updated them of course.