I really think these torpedoes need to be looked at. Having tested them in the last few days maxing them out they fall behind all others by miles. This is how I suggest you fix them:
Make their damage equal to a photon torpedo since they already have a longer CD. Then instead of the 20% extra penetration add this to the effects instead. "Has 2.5% chance to completly bypass shields.
Right now these torpedoes are useless and its not really surprising that everyone uses quantums. All the other topedoes in fact (especially plasma) need the same loving. Especially because no way to obtain other types apart from drops.
I started trying them out recently and I too hope that they get a little boost. The 2.5% suggestion you made is a bit low considering that this is a projectile weapon though. Perhaps a proper boost for them would be to increase their damage yield by ~25-30% and replace their buff with a 20% change to completely bypass the shields, meaning that every 1 in 5 torpedoes will just go right through the shields and hit the hull for full effect.
The transphasic torps have a net penetration of about 28%. I'd suggest to raise the penetration to an amount, where you need similar amount of time killing a ship by pounding it with 3 transphasics like by pounding it with 2 photons + 1 single cannon (without shield redistribution).