The damage buff to Transphasic Torpedos from the Breen set is not very large, and not commiserate with the loss in durability of not having 3-Borg + MACO shields.
Pointedly, while two transphasic high-yield volleys may do a combined more damage than one quantum HY volley, the time between makes it so that the target can quite easily out heal the damage. The best way to think of Transphasics is as a hull-hitting pressure weapon. If the enemy team has a large amount of cross-hull healing available, then your damage should amount to very little. If they are starved for hull heals, you have a reasonable chance of wearing them down, if your team is built around shield-bypassing attacks.