I have, I changed the .ini file for my map to make the EYE (Adv. Comm. Center) capturable. It does nothing. Now if I make the player GDI and capture it, I do get Ion Cannon. So there is code saying that when you capture it as GDI (even thought it is uncapturable by default) you still gain Ion Cannon. This is why I believe there is a code preventing Nod somewhere probably saying this:
Superweapons:
PlayerisNod?
if 1 then:
Ion Cannon=0
Something like that. In other words, as long as this code exists (and I'm almost certain something along these lines it does), then I cannot give Nod Ion Cannon. Funny thing is, even if you are multiplayer 1-6, if your tech tree is of Nod, the same still applies if you catpure an Adv. Comm. Center, you get no Ion Cannon as Nod. Hence further enhancing my postulate that this code exists forbidding the Nod Tech Tree Ion Cannon access.
Now the brilliant part is that even by creating a copy of the Adv. Comm. Center ([EYE2] for example) and let Nod have it in their tech tree (what side can build it), you still can't get Nod to use, OR build the Adv. Comm Center. Which makes me believe the code preventing Ion Cannon is hard wired into the game engine.