I was about to write about fleets and flawless victories, but intrinsic_parity wrote much of what I wanted to write.
It is not so much about recovery of enemy ships, it is about recovering your ships if they die, especially if they had s-mods.
If my ship that died had no s-mods, no problem, I just rebuild it if I have the blueprint. If it has s-mods (or I cannot build the ship), I am not scuttling it! If I have Field Repairs and nothing else to fix, I will recover it and lug it around until the d-mods disappear. Otherwise, I reload and replay the fight until the result is flawless victory (or I give up and do something else like cheese trade until I earn enough to upgrade my fleet) because it is faster that way. There are exceptions, like if I lose a small ship or two in an endgame fight, fine, I did not lose that much money and I eat it.
However, Field Repairs makes it tempting to recover anything that does not have more than one d-mod, and it is more convenient than shopping for one at a core world or waiting a month or two for my Orbital Works to spit one out. And if I am fighting exotic ships I cannot build or buy, I will recover (and mothball) at least some of them. And if I am running around with Ziggurat, and it blows up, I am not spending nearly two million to fix it. Either I let Field Repairs fix it, or I reload.
I will just restore everything. I would much rather pay more up front for a pristine ship that will not die and will have better combat power per deployment point.
If I think casualties is likely, and the only significant reward is money, then it is better to avoid the fight in the first place and run drugs or otherwise cheese trading exploits - much safer!
I dislike d-mods, and I strive to have every ship pristine at all times. I have a special fondness for Field Repairs. I plan to take Hull Restoration so I do not need flawless victories for fighting to be profitable. I will only respec if I need to enable flagship Radiant to be the best it can be with more combat skills, if I go for the Tech 8 path, or if I really need all combat skills to enable soloing fleets efficiently like SCC did with phase ships.
Does it even work like that though? To me it sounds like the chance to avoid D-mods completely only applies to your own ships, not enemy ships you recover. Those only get a chance at -1 d-mod at most, and even pristine ships get at least 2 when destroyed.
With Field Repairs and other Industry skills, I sometimes see formerly pristine enemy ships with a single d-mod. They are worth recovering. I obtained most of my capitals by recovering and fixing them with Field Repairs. By the time I raided for all the blueprints, I already obtained most of my endgame fleet by recovering them from the enemy. It was also nice recovering spare Radiants with one d-mod and field repairing them for later.