More specifically, a lot of fleets wouldn't even have access to a large turreted slot of the right type, whatever that might be.
I'd say that that is something that should be both techs, just different mechanics, and perhaps a fighter that has that specialty. I agree that it'd be bad if it was just one weapon, but we have one already in Energy and I still think the Haephestus needs a distinct role.
I feel the same way about this issue, mechanically, as I do about fighters; I want these mechanics to be very functional unless they're countered, in which case they shouldn't work very well at all.
Trying to balance all vs. all is a road to mediocrity, because then we're generally going to find that these things get nerfed to the point that they are marginal uses of resources at best (see: fighters). I'd rather that some fights be broken both pro / con and for players to have to diversify their fleet compositions to handle the counters well, personally. I wouldn't mind at all that Faction A can be beaten with missile spam, but I'd love to see Faction B kick your butt if you tried it.
I'd really like to see Factions that went all Macross-spam and make players handle that if they tangled with them.