I'm sorry, but the problem seems to be poorly presented. How is it "OP AF"? What is the reasoning behind needing to nerf it?
The way I see it, having ships that are more impactful in the hands of an experienced player is just Starsector's way of delivering a balanced challenge.
Enemies in this game, generally speaking, get larger fleets with no need to worry about upkeep logistics, or having to make sustainable builds for consequent fights and mitigating casualties. They also have access to ships that are broken by design as they are meant to represent bossfights (Tesseract, Radiant, Ziggurat) with player getting either gimped versions of the originals, or none at all. The AI also has more global control of the battlefield, with units utilizing lines of sight and covering each others retreat by putting constant pressure with freshly vented vessels as the damaged ones regroup.
The player, on the other hand, gets worse AI that only functions as a collection of individual units that loosely follow a limited selection of commands with, and not as a team, while the outcome of their command execution is always unreliable and uncertain, on top of having limited and more balanced fleets due to having to plan ahead and be prepared for any kind of engagement, all while being severely restricted by all logistical problems such as resource upkeep, deployment recoveries and fleet limits. Also, all the more impactful ships (Doom, Ziggurat, Radiant in your AI fleet, and so on) require significant investments into skills that effectively cut you out of options that would further improve your fleet.
All of this is counterbalanced by the fact that player has excess of control over: 1) selecting the best capital ship with the best build to make the most impact with their personal skill, and 2) fully customizeable builds that let them select the best tools for the job, thus building fleet compositions with overall better performance to further tilt the scale of battle in their favor.
So, the way I see it, is that OP takes issue with ships (that are only effectively spammable by enemy AI, and not in vanila player's fleets, specifically, mind you) that perform better in players' hands than they do in AI's. This is where I'd need further elaboration, because I fail to understand how the ability of skill application is a problem in a game that takes skill application as part of core challenge balancing, and already has built-in ways to counterweight it on the enemy side?
All and all, I am mostly left with my assumptions, since the entire topic was a blanket statement, and we're left with only guessing the reasoning behind it. Hope I helped OP with defining the framework, and they can start there, or they can present it in completely different light that I've missed, but far as I can say right now, Doom itself isn't really an issue here, since it's the player's hands people seem to be concerned about.