Yea the thumper is in a really weird place now, all things considered. Against an enemy with even 200 armor and 10 residual it's doing significantly less than it's stated dps, and against anything in the 400+ range even when stripped it's dps falls into heavy mortar range.
In comparison to the heavy mortar it's far less effective against anything with real armor, but it gains a ton of effect against missiles and fighters while retaining the ability to scare low tech frigates silly. The problem isn't that the thumper is bad, but more that the thumper's greatest niche (punching down at lower tech frigates and light destroyers while also being effective PD), is overshadowed by two factors.
1. Low tech frigates are usually not a high priority on the players mind, and the ones that are will be high tech ones that have an efficient shield to render the thumper moot.
2. The flak cannon is the best PD weapon in the game and right in the same price range, skewing the benefit of taking a thumper for any joint PD work.
It would be very hard to make the thumper more effective against hulls without seriously infringing on the heavy mortar's territory. Over all I think it's a weapon that doesn't have to extend it's usefulness against late game fleets, it's fine to have a weapon made to be good earlier in the game and against lower tech fleets like pirates and luddic path especially earlier on.
Honestly, I think the OP of the thumper should be reduced to near zero to represent how cheap and easy to clean it is, and that's it. Maybe 2 or even 3 OP, basically a free slot. That would remove the need for it to feel like it needs to be equally as relevant as the flak or mortar.