I like this a lot. It solves the awkward Extra Munitions upgrade, having to go into a Torpedo slot (when, thematically, it might as well have gone into a Missile or Bomb slot). Makes a lot of sense to put it on the variant and to use it to calculate the variant's upgrade cost.
In the image above, does this mean you can have two different missiles, and one of those missiles gets basically an EM token? I like that, but you have to figure that that will start to overcost an additional missile. How to explain this... hmmm. So, say you equip a 4 point Cluster Missile in that slot, and that gives you an EM token, so you effectively have 2 Cluster Missiles for the price of 4 points and the variant card (whatever it may be... 1 point, 2 points, etc.). Another missile you upgrade will come at a steep increase of its own cost (say, 3 points for Adv. Homing Missile, or Ion Pulse Missile). That's a lot to pay, relatively speaking, when you got basically a second Cluster Missile for only the cost of Variant. In this regard, I suspect that the second missile slot will go unused, except by cheaper missiles (like the XX-23 Thread Tracers). It would not make sense, economically speaking, to put another 3 or 4 point missile in that slot, so consider that you're basically relegating that slot to a Thread Tracer Missile in almost all cases. (A way to cure this would be to make both slots blue, or to give a native discount to higher-end missiles which go into white slots. Say, "If you equip a 4-5 point missile in the white slot, decrease its cost by 1 point", although I'm not sure even that would cure it).