Better ships are generally more expensive, and last time I checked, D-mods affect price.
Generally, but not well enough to tie another system to it. For one Derelict and Remnant ships are not well balanced in terms of price
at all (literally Guardian = Radiant = Paragon =
Dorito Bag, according to the price list), and you can get bounties against those kind of fleets through contacts. There's also the fact that station modules all have separate prices listed, and every last piece costs the same as a Paragon no matter it's actual function. I don't think a t1 midline pirate base should be worth...one station, two modules, four structural spurs...3.5 mil, or seven Paragons?
D-mods do effect ship price, but there are d-mods which don't effect combat at all (Erratic Fuel Injector, Degraded Life Support Systems, etc.) and some d-mods make a
lot more difference on some ships than others. Or even none, depending on loadout. I can't test it but I assume it's possible to get, say, Degraded Shields on a ship that normally has shields, and than outfit it with Shield Shunt. To say nothing of what Derelict Contingent does to heavily d-modded ships...