Here's an out-there idea: make strategic subs T4, give them powerful long range torpedos, and leave their tac missiles and strategic missiles as is. Cybran has stealth and maybe slightly faster move speed, Aeon has a shield, UEF has jamming + more hp. Sera probably needs something here but not sure what tbh. Buff their t3 subs damage and health and increase its cost? Give them their own strategic sub? Not sure.
To go even further, add one more minute to the nuke build time and make it the same damage as a land based nuke, but now it takes two extra minutes to build and not the current one extra. The nuke sub nuke arbitrarily doing less damage doesn't make much sense and isn't something a new person might realize.
Something key here: most of the balance and cost for this would be around them being powerful long range torpedo support. The nuke and tml are, to an extent, fun extras. I'd want this unit to be able to be built with no intention of using the nuke. The nuke is to mostly make it viable after navy is won, like battleships are with their shore bombardment, and the tml is just too fun to snipe SMDs with when they're not paying attention to get rid of.
My issue with billy nuke subs is basically that I think as soon as the first one is fire you now have a very tedious back and forth of building and sniping tmd or having enough cruisers in the right spots which sounds not super fun to play. I also think billy subs would be very apm intensive to max their value and high level navy play is already highly apm intensive imo.
Quick edit: To be clear I would not be for normalizing damage between nuke subs and static launchers without increasing the build time by at least a full minute, and that's at a minimum. Way too strong otherwise imo. Also, I suppose this wouldn't necessarily have to be a t4 unit.