Actually, in a lot of ways this would greatly improve the effectiveness of Torpedo Boats, as well as expanding their options RE: DOffs. Since the fire-rate of torpedoes increases, having multiple launchers becomes an asset as you'd be able to sustain a potentially tremendous amount of pressure. Even one launcher would actually be potentially threatening even without a power.
With 3 PWO-Torp DOFFs you can already fire at the same rate as the Omega...without the cooldown.
If you had 4 Omegas - you'd have to turn off autofire and keybind each of them separately - otherwise you'd only be firing the first one until it went on CD - then you'd fire the second, etc, etc, etc.
You'd never likely run more than two torps - you'd have two keybinds, Torp #1 and Torp #2 - running one when the other is on CD. At which point you're looking at dropping in two DHC.
So basically it's a case of being able to do away with PWO DOFFs while running a pair of DHCs - or - going three DHCs, using PWO's to reduce the recharge.
So where exactly is the torpboat? You're basically just running your standard rig with better torps. That whole cake and eating it thing. It's a case of wanting to avoid the plasma resist of the STF shields, by not using the Omega but using another form of torp that does not suffer that "penalty"...
Torps have their place. It's no different than avoiding DHCs on a boat with slow turn or running DHCs on the escort instead of arrays.
If you're putting a torp on your boat, you're putting it there for a reason - whether it's for one of the effects, for hitting that naked hull, popping a target with full shields, etc, etc, etc.
It's no different than any other weapon - they're not all the same - they're not all as effective in every situation...
Omega torp was designed for cruisers. You let it reload while broadsiding and once the enemy shield is weak bring it to bear for it's burst. People trying to use it on a torp boat, or with torpedo abilities are missing its original design intent. Granted if it works in that role or not is still undetermined.
The 4x DHC popularity is simple due to the much lower opportunity cost of using 4 DHCs with turrets when compared to using 7x beams, or any other weapon really. Because the first DHC will fire every shot at full power, while the other weapon types aren't quite that lucky.
Sci torp boats are a necessity of needing maxed AUX to have useful Sci abilities (for the most part) combined with the extreme importance of having a high shield power. Something has to give and for most the opportunity cost is just packing torps and hoping for the best.
But in the end I think torpedoes are fine how they are. Really it is the other parts of the game and how they function that makes them under desired more than how they themselves work.
Increase the energy dmg resistance rating of armor consoles so energy weapons become less effective against hulls (4 neutronium consoles stacked should give 80% energy resistance. point.). At the same time, keep the kinetic dmg resistance at a low level.