Yep, if you compare Enforcer to Hammerhead, you'll notice that flux capacity & dissipation are almost identical. And we're comparing a Mastery and a Core epoch ship here.
You probably shouldn't directly compare the total flux capacity and dissipation; rather, the capacity and dissipation per weapon would be preferable. As far as flux-using weapons go, Enforcers have 5 mediums (~10 small mount equivalents or SMEs), while Hammerheads have 2 mediums (~4 SMEs) and 4 smalls. Therefore, Hammerheads have 525 capacity and 31 dissipation per SME while Enforcers have 400 capacity and 20 dissipation per SME, at least before adding vents and capacitors. It should also be noted that Hammerheads have roughly twice as much effective shield strength as Enforcers due to shield efficiency, so even if you factor that into the capacity per gun the Hammerhead's probably still coming out ahead in usable capacity and venting per SME. If the Hammerhead's two small missile mounts were changed to small universals, it'd have 420 capacity and 25 dissipation, which I would agree might be insufficiently superior to the Enforcer's flux statistics.
As further points of comparison, the Eagle has ~588 capacity and ~31 dissipation per SME, the Dominator has ~476 capacity and ~21 dissipation per SME, the Falcon has ~700 capacity and ~35 dissipation per SME, and the Venture has ~1170 capacity and ~50 dissipation per SME, while the Sunder has ~590 capacity and ~36 dissipation per SME and the Medusa has ~545 capacity and ~36 dissipation per SME (improves to ~667 capacity and ~44 dissipation if the universals have missiles), ignoring missiles when adding up SMEs. I would also point out that the Hammerhead is hardly unique in being a more advanced vessel with little overall (or sometimes relative) improvement in flux capacity and dissipation; compare, for example, the Wolf and the Lasher, or the Odyssey and the Conquest.
The Hammerhead's flux statistics are reasonable for its armament and are a reasonable improvement over those of the Enforcer given the differences in armament; it's just that its armament seems a bit inadequate.
As far as improving the Hammerhead's armament without significantly changing the sprite goes, I could perhaps see upgrading the rear small energy mounts to medium energy mounts or putting a medium mount on the stern section somewhere in the middle (preferably somewhere that looks like it's raised enough to fire over the bow to keep with the Hammerhead's preference for head-on engagements). Or perhaps giving the Hammerhead another two small mounts on the stern section, just ahead and a bit inward of the existing pair. However, I feel it should be noted that the Hammerhead's armament is not all that much worse than the Medusa's; both vessels currently have the same forward fire concentration (two medium and four small mounts), with the Medusa's biggest advantages being that it's not limited to missiles in its two fixed small mounts and its mediums have decent arcs. The Medusa's generally superior mobility and shields tend to further exacerbate the difference since it's less necessary to put PD in the two forward small energy mounts and the Medusa can probably stick around a bit longer, depending on the exact armament chosen.
(Note on SMEs: I understand that these are probably not ideal units of comparison. However, the average ordnance point cost and flux per second of weapons roughly doubles with each increase in size category, so it's not exactly an inadequate metric to use when comparing those hull statistics, especially when you don't know what weapons are actually going to be mounted.)
Four medium hard-points by replacing the missile ones (and better flux stats). That way mixing damages can become a thing and nobody will even think about crossing it's bow.
I am of the opinion that four medium mounts on the Hammerhead's bow would look overcrowded. The Eagle's bow is about the same width and the three medium ballistics it has there are just about touching each other; same is true of the mounts on the Hammerhead if you put missile racks in the small missile mounts. I could see three medium ballistic mounts on the bow, which would still leave an adequate number of mounts for mixing damage types without the ammunition issues of using missiles, but that basically makes it the same as the Enforcer but with a more narrow cone of fire.
Okay, here's a radical suggestion to bring Enforcer back in line and make it less prone to derp-AI at the same time: Make it shieldless.
Frankly I think that would just be a straight up buff for the Enforcer. The one thing that stops AI enforcers from rolling over everything is bad shields. An Enforcer that uses it's entire flux on powering its 5 medium ballistics mounts (what an insane number for a destroyer) would be stronger than ever.
The Enforcer's shields are probably its biggest weakness in the hands of the computer, I agree with that. However, I'm less inclined to agree with rating the Enforcer's gun power at 5 medium ballistic mounts, especially if it's without shields, because you almost have to put flak cannons in the two medium ballistics on the flanks since it otherwise has little or no PD coverage.