Well, I think it's made explicit that Ikana lost the fight against the enemy nation, as Skull Keeta says;

And the spirit of the King and the Garo ninjas remain behind simply because they are filled with regrets.
If you notice, the King and his seravants are actually skeletons, which points out that they're not alive in the Human sense of the word.

I take it as their skeletons are still being re-animated by the magics of the Curse that was inflicted upon them when Majora's Mask caused his chaos with Skullkid.

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