Observed from the Harbinger having its mounts changed from synergy to energy, but expanding the discussion to all ship configurations and loadouts in general.
While I think Harbinger should really be nerfed hard because it is extremely overpowered, I feel that the current configuration of energy hardpoints is illogical, and is not something that actual ship designs would have made.
In the real world, designers add strength to strength, so that the strengths complement each other to make a powerful system. While at the same time, the components that make up the whole system don't have to be individually overpowered. Take for example, ballistic missile launching nuclear submarines, combines strategic mobility, stealth, and nuclear missiles so that the missiles they launch are difficult to counter.
The old Reaper Harbinger, despite being excessively overpowered, is actually something that realistic warship designers would have made. It combines low-flux missile weapons with phase ship mobility, as well as explosive missiles with the ability to ignore enemy shields. It's like if the ship designer went around and said: "Hey I got this fast ship that has an engine which generates flux, but can ignore enemy shields, what weapons should I put on it? I guess it better be some missiles that don't generate flux and deals explosive damage cuz enemy shields won't be worth a damn"
The new energy hardpoint Harbinger feels too obviously as nerfing for the sake of nerfing, without giving enough to the back story or principles behind the design. Because flux generating energy-type damage and phase ship mobility and ability to ignore shields don't synergize. It'd be like if someone in the real world designed a nuclear submarine but made it so that it could only use machine guns, or someone designed an agile jet fighter but made it only able to fire torpedoes.
I imagine that in the game universe, if someone come up with an energy hardpoint Harbinger, either his boss or his customer would say :"Gee, can you swap those energy hardpoints to missile hardpoints for me? It's not like my ship is going to be pounding down shields, with that disruptor already mounted on top." And then, the designer probably changes hardpoints to missiles.
I think if a ship needs to be weaker, it should have more realistic weaknesses grounded in its back story. Take the Harbinger example, maybe the disruptor takes a lot of power to run, so that the ship's flux dissipation is very weak. Or maybe the disruptor array takes up alot of space, so the ship has fewer ordinance points. Or heck, maybe the Disruptor overloads the Harbinger at the same time as it overloads the target, so that it can't follow Disruptor right up with Reapers. (Disruptor interfering with antimatter containment fields in missile warheads? Sure, but then why can't you put normal explosive rockets?)
On top of that, there's quite a few loadouts that don't play to the ship hull's strengths. Like why Hyperion wouldn't always be equipped with strike weapons? If someone just wanted pulse lasers, he wouldn't have put up with the expense of obtaining and maintaining a Hyperion. Or many of the short ranged weapons being equipped on slow ships that couldn't close the distance to actually use them.