Major plot hole with Heavensward ending (Spoilers, duh)

[Allyrion]

Odin is a Primal and an Eikon, Eikon means false god for garleans so all the primals are Eikons.

Eikon is just the Garlean term for Primal. They're on another continent, makes sense.

I think the OP's problems have been explained away already, but yeah basically, when Niddhog's eyes were first taken, he was still alive. The dragon eyes seem to be a pretty endless source of aether it seems, I don't think they can be "drained" in the same way say a crystal could.

I'm guessing you all haven't started the extreme primal quest line.
The term predates the Garleans and the story makes a distinction between Eikon and Primal.
We do know Eikons are not the same as PArcher said, but may be related or similar.

Edit: wasn't Odin revealed to not be a Primal, but an eikon? While we don't know just what the eikons are, we do know they aren't actually primals like the Garleans believe

I'm not sure this is stated outright unless it's further into the EX Primal quest which I haven't done yet.
Odin is seemingly different, at any rate. It wouldn't be hard to believe he's actually an Eikon (maybe the only one we've met).

[Kaiser-Ace]

The Rhongomiant was Arthur's Spear. It was one of his armaments along with Carnwennan (His Dagger), and Caledfwlch (his sword). Caledfwlch being better known as Excalibur.

EDIT:
Forgive the repeat of data, I posted at the exact same time as your reply to Cilia, Jonny.