This is exactly why I play on "cross-planet attack" mode, because I really like Ion Cannons, and I'm not foolish enough to ignore how useless they would be if owning them increased the wave size against that planet; that's kind of counter productive isn't it?
Sure, you can make the argument that you don't want them on the "outer" planets, but then what the heck is the point of having them? A good defense consists of making chokepoints which the AI can't easily penetrate. You simply don't have enough turret supply to defense up every planet even if you wanted to, nor is spending the knowledge to do so efficient if you are trying to win the game. In addition, having an Ion Cannon on an "inner planet" seems pointless for 2 reasons:
1. Ion Cannons should be covered with shields or they will die very quickly to an assault.
2. Why would you waste a valuable shield on an inner planet that shouldn't be getting attacked anyway?
Ion Cannons on a planet should be (from my perspective) a good incentive to capture that planet and turn it into a chokepoint. There is a "natural" defense on that planet (similar to a mountain in another game), that gives it merit as a defensible position which you want. From a player standpoint, we are being punished for making what should be a solid tactical decision on our part.
I understand that you want there to be a drawback to having Ion Cannons, that is completely acceptable; but the drawback should be something logical that is easy to grasp and is consistent with the flow of the game.
It doesn't even make sense that the AI would send 10x waves to a planet with an Ion Cannon. I once had a planet with 3 Ion Cannons which said it had 60x waves coming to it. As a logical player I ask myself the question, "If the AI can send 60x waves to this planet, why don't they just send 60x waves to any planet?" So from a design perspective, it makes sense to you as a discouragement from taking the Ion Cannons, but from a logical and story coherency standpoint, it makes no sense at all.
If you want to discourage players from taking Ion Cannons, why not just give them a massive energy cost? See, that makes sense to me. Here we have this extremely powerful weapon that the AI built, and costs 300,000+ energy to operate. I can't have very many of them because it will cause my economy to crash, so I have to only keep the ones I can afford. That's a way you can keep them in the game, but discourage players from using them, without hurting their tactical options or hurting the game from a logically coherent standpoint.
Edit: Also, you can circumvent abuse by preventing the Ion Cannons from being able to be "turned off", a la saving energy when you don't need them.