It's on the theory board, therefore, it is a theory. It would explain their later abesences. And it's a bit odd that Zora King and Mido are sad at the ceremony. And Nabooru mystical disappears (No black magic, Like seen at the end of the Spirit temple as a child and PG Battle) and is said she haunts Gerudo Desert. (Straight from a gossip stone)
The word "haunts" is not used in that context; it can't be in that context, because it's likely that you find that Gossip Stone before she gets deep inside the Spirit Temple, when you are still a child.
Gossip Stone by the Desert Colossus said:
They say that the thief named
Nabooru, who haunts this area, is
a Gerudo.
Observe different interpretations of the word "haunt" below:
haunt
[hawnt, hahnt; for 10 also hant] Show IPA
verb (used with object)
1.
to visit habitually or appear to frequently as a spirit or ghost: to haunt a house; to haunt a person.
2.
to recur persistently to the consciousness of; remain with: Memories of love haunted him.
3.
to visit frequently; go to often: He haunted the galleries and bars that the artists went to.
In order for the statement to make sense when you read the Gossip Stone, it has to be the third meaning of the word, to frequent. That makes sense, as she visits the Desert Colossus because she is in charge of that Temple.
Nabooru doesn't disappear; you find her brainwashed inside Iron Knuckle armour after you defeat her, right before the Twinrova boss battle.
The reason that Mido and King Zora appear sad is because they never learn what happened to Saria and Ruto, respectively. King Zora and Mido never see them return to their homes, because the Sages awaken in the Sacred Realm. They are seen for the first time flying overhead King Zora and Mido in the physical world of Hyrule, and Mido and King Zora look up, and seem to get a sense that the ethereal beings were Saria and Ruto. Shortly after, they re-materialize into their normal forms. This is just a demonstration of some of their power as sages, not an indication that they are ghosts or were ever dead.