In the same hypothetical where both sides have equal tech and tonnage? Yeah, under those conditions the victory would probably go to whichever force was better-optimized for missile combat.
Do take all of that with a grain of salt, though, because that situation is actually fairly rare in practice. Most of the time tech and tonnage won't be equal, so you might end up in a situation where your fighters can't deploy, return, rearm, and redeploy enough to kill more advanced ships closing with your carriers, or where your missile ships are forced to retreat because they can't break through the enemy PD reliably.
Also worth noting that a lot of this orients around the idea of fighting against another human player who is aware of all this meta-stuff. Against NPRs and the three threats you can get away with just about anything, since they don't optimize intensely.
I've probably argued this point before, but in my experience hyper-optimizing everything gets pretty old after a while. It's much more fun, IMO, to throw together ships that seem fun and look like they were actually designed by committee and built by the lowest bidder. Beyond real basic shit like square warheads and matching jump drives to ship tonnage, anyways.
You can still make early-ish fighters and missiles, but the drive rework hit both hard (particularly fighters, IMO), so they're a lot less dangerous in the TL1-3 range. That's where E/KWs can really shine, since everything is already fat and slow & missiles are both markedly less effective and more dangerous to rely on (both because fewer are generally carried and because magazines are more likely to pop when hit).