If all Pather ships have Ill-Advised Modifications, you can forget about using them to fight. Weapons *WILL* break and go offline permanently, often before you score your first kill. The only ship that can get away with Ill-Advised Modifications is the Mudskipper II due to its lone heavy mount.
As for destroyers:
I would not use Safety Override on Medusa. It is too fragile and lacks ballistic firepower to crush shields as quickly as more heavily armed Enforcer or Hammerhead. Medusa has two useful endgame weapon configurations: two heavy blasters plus possibly two railguns (light needlers are too expensive, must have enough OP for flux stats), or two phase lance (with Adv. Optics) and two light needlers.
Variation of the Elite Enforcer is a top-tier endgame destroyer-class ship. Safety Override with HMGs and Assault Chaingun is okay.
I still think Hammerhead is rubbish, if player does not want a Safety Override ship, due to being an inferior Enforcer knock-off. The best it can do is two LAGs and two medium kinetics of your choice. Two Vulcans for PD is no substitute for Enforcer's two (dual) flak. Because of that, Extended Shields hullmod for 360 shields is almost mandatory for Hammerhead, and due to lack of OP, it hurts when I have to choose between that or another option, such as enough capacitors to not self-destruct with the ammo feeder system. I do not need to make such vital decisions with either Enforcer or Medusa. If Hammerhead had more OP, it can use Mauler-and-HVD combo backed by two tactical lasers, but it does not have enough OP to make it work without sacrificing more important hullmods to keep up with its peers. For Safety Override, HMG, Assault Chaingun, and two Ion Cannons are brutally effective. Finally, while I have no problem fitting two to four missiles of my choice on an Enforcer, I have so few OP with Hammerhead that I usually put two 0 OP singletons on the Hammerhead.
Assuming fleet burn speed of 9, I prefer Gemini over Condor because it has good cargo capacity and can standoff somewhat decently with Mauler and HVD even without ITU. (One of the few ships I do not use ITU on due to crushing OP shortage.) Condor's only use is if you want a carrier with burn 10. Even with obsolete fighters, bringing a Gemini is still tempting due to cargo capacity and viable combat ability. Yes, it eats quite a bit for a destroyer, but that is often not a problem due to the change from Logistics to 25 ship limit.
EDIT: Harbinger - I think it is too expensive to be worth using, at least for energy weapon beatdown. I get more out of two Sunder or Medusa for similar cost.