I don't think they are apparitions, otherwise they would have stated that in the HH. maybe that game you are hoping for will feature how K&K come back.
You raise a good point but in many areas concerning the minor games, the HH provides a perfunctory description of the narrative's aspects, quickly glossing over them without second thought.
Concerning the
Oracle Twinrova, this is all it has to say,
Hyrule Historia said:
The foster mothers of Ganon once known as the thief Ganondorf. Ganondorf became Demon King Ganon and Twinrova are now trying to revive him.
Browsing online, I did find the suggestion that Koume and Kotake die in a manner different from other OoT's bosses interesting. Rather than disintegrate into ashes, the two are transported away by blue beams resembling those Link leaves dungeons through. While the halos above their heads are certainly suggestive of death, perhaps they possess hidden special powers which could also explain why the two lived for around four centuries.
Given the
Oracles' placement on the Decline Timeline after
A Link to the Past, it's also likely Ganon used the Triforce to revive his surrogate mothers after conquering the Sacred Realm and transforming it into the Dark World.