They do standard damage against shields, just at a lower rate of fire. However they do exchange in that they do about 30% (50% crit) in bleed through damage to a hull where energy weapons only do 10% (20% crit). My base loadout is two phaser + PTL forward for the shield strip. Two PTLs + phaser aft. The aft is good in that I have a turret on the aft phaser so I can use it to take out fighters or just find a quick target. However TLs as far as I've seen don't rely on your power settings. So if I'm in trouble I can switch to defense mode and let my shields recharge while beating the hell out of anyone trying to follow me. Even better since anyone following me has to keep their forward facing me and it means I'm only having to fight one shield front rather then two or three in a dogfight.
As for my DOffs, I use defensive ones. I have seven shield repair keys, two instant heals for my ship and two SIF styled keys. Been in a number of spots where I've lost all shields and been down to about 20% on my hull. I just click about ten keys, I'm back to full shields twice over, have 2x damage res for 15sec and have a ship that is back up to 60% hull. In 30sec I get to do it all again. The hull repair is every 20sec so i just spend a lot of time clicking that.
"Oh I just took a crit hit, magic reset button."
"Oh no, I just took another crit hit, magic reset button."
Jinsei wa cho no yume, shi no tsubasa no bitodesu