In my opinion, the problem isn't that missiles themselves are particularly out of balance, the problem is that they need to compete directly against more broadly useful options.
There are quite a few weapons that have the same problem; they exist to serve a particular utility, but you don't run into that very often, so it is rarely a good idea to try using them.
And I don't think just making them stronger is a good solution. More often than not, this only results into weapons that do exactly the same thing with different visual effects, which isn't what you are after, either.
Missiles, in particular, I think would largely benefit from being equipable in utilities slots. They serve functionally the same purpose; consider, for example, a small Seeker missile rack, which has 16 missiles. That is on broadly the same level as chaff as far as how often you can use it. So why not just make it a utility?
Plus, since Shield tanks generally put their own utility slots to a more powerful use, offering alternative utility options would make hull and hybrid tanks more powerful by comparison, since they could get more out of their utility slots than an equivalent Shield tank.
So not only do you make missile racks more powerful and useful, you also make other alternative build Styles more powerful and useful. Seems like everybody wins!
