Current Thumper is still is doing a 500 damage burst against shields which is pretty good, and is a nasty thing to fire into a swarm of fighters, while nuking stripped armor ships pretty good up until you get into very heavy armor categories.
You really don't need much armor to neuter the thumpers DPS. 500 armor (hammerhead) is enough to half the dps to hull. For any armor over 880, heavy mortar has straight up better hull dps in addition to way way better armor penetration. Those aren't particularly heavy armor values. For anything more than a light destroyer, its at best marginally better, and at worst significantly worse than a heavy mortar in hull dps, which is where it is supposed to be strong. At low armor values, it does lots of damage, but those are also the easiest ships to kill, so it makes little sense to devote an entire weapon just to trying to kill them a bit faster.
Also, efficiency is much more important to shield damage than burst. If you do a burst to the enemy shields, but you effectively do a bigger burst to your own shields, you're gonna lose the flux war. Burst isn't bad against shields per say, but inefficient burst isn't really a good thing: you're usually hurting yourself more than the enemy. Especially if you consider the ships that the thumper goes on, they generally have pretty mediocre or bad flux stats, and they really can't afford to be trading at 1.2 flux/damage. Burst matters more for HE/Hull because you only have short windows to deal damage and its usually worth trading your flux capacity to deal damage faster.
Personally, I really don't like the idea of making the thumper better against shields, that takes it towards the other weapons in the balance space and just makes it an alternative generalist weapon option for ships with really strong specialist options. I would much prefer the thumper (and frag weapons in general) be aimed towards being specialist finisher weapons that also provide a bit of shield pressure. Something like switching the damage from 100x20 to 200x10 effectively gives the weapon an extra 70-80 hull dps at most relevant armor values without changing the shield effectiveness.