Actually, the reason of her being a spirit monster in Gishki is, according to Master Guide, Noellia uses a spell on her (from Aquamirror Illusion art), that allows her to separate her physical body and her spirit. So she's not really dead. Her spirit form transforms into Evigishki Merrowgeist, while her physical form transforms into Evigishki Gustkraken. So I don't think her being a spirit monster in Gishki has to do anything.
Moreover, Master Guide also said she's defeated in a war, and in the art of Aquamirror Cycle, Noellia is reviving her. So this confirms if she's not a spirit anymore.
In the Necloth version of her, she's also not a spirit monster. However, in the new Necloth Ritual Spell, you can see Emilia holding a golden crystal, probably it might explain as why she could keep her youth.
Or, the timeline confusion. Probably that Emilia we see isn't her in present form. Though I feel it's unlikely.