Pretty much this is the only hurdle whenever I’ve looked at Aether pets that involve Necro - you can pick up Elemental/Physical->Aether for pets and your Skeletons, Blight Fiends and Reap Spirits all still have that side Vitality damage (and Acid for the Fiends but it’d be weird to only have conversion for them/that). Soul Harvest as well remains Vitality for pet damage.
Aether pets with a focus on Shaman should be mostly fine though - Briarthorn, Primal Spirit and Mogdrogen’s Pact get full converted, you can also opt for a pure Aether Chillmane Yeti and pure Aether Swarmlings too. You do miss out on converting Blood Pact though. There’s a beginner guide for that here:
And TPOM did Aether pets Vindicator awhile back here:
Occultist pet focus looks mostly ok as well - Familiar and Storm Spirit can be converted to Aether. Hellhound’s Physical and Fire also gets converted, on Hellfire, the flat Fire does too. Only the Chaos damage on Blazing Death, Hellfire, Ember Claw and Infernal Breath remains. That said though, I think Shaman is more suited for Aether pets than Occultist is.