Huh. Definitely some different opinions here...
My personal opinions (context note: I do tend to have all the relevant industry skills):
Any logistical d-mods on a civilian vessel = trash it. The purpose of a freighter is to carry as much cargo or fuel as possible for as low a cost as possible. None of the d-mods are worth it here.
Increased Maintenance = if this is one d-mod out of many, it's probably okay; if it's the only d-mod, not acceptable. Late-game, some exceptions may be added for smaller ships; IM on a Tempest isn't a big deal when you've got cruisers or capitals, for example.
Degraded Engines = Varies heavily by ship type. On something that lives by its speed, or on something where the reduced burn is a problem, this can be a make-or-break on whether a ship gets restored/scrapped or used with d-mods. There are some hulls where it's a non-issue, though.
Unreliable Subsystems = Varies heavily by ship type. On a frigate or phase ship, this is a hard no. On most cruisers and capitals, I don't care. Destroyers vary depending on where I'm at in the game - though, okay, late game I don't use destroyers much anyway.
Structural Damage, Compromised Armor, Compromised Hull = Varies by ship type. On phase ships, hard no. On low-tech ship types that rely on armor, these are all probably a no. On high tech ships that rely on shields, I'm happy to have any or all of these.
Phase Coil Instability = hard no for a flagship, don't care for AI-run phase ships; they tend to do a lot of loitering uselessly in phase, for which this d-mod mostly balances out.
Damaged Flight Deck = mostly don't care; may be worth fixing for a dedicated carrier, but it's not a big deal (at least with the way I equip and use carriers).
Defective Manufactory = Varies; this is a hard no for dedicated carriers, but a non-issue for things like a Tempest or Odyssey where the fighters aren't really the point.
Malfunctioning Comms = I'll cheerfully take this one. Honestly, there are cases where I'd be willing to spend ordnance points (albeit not very many) on reducing fighter engagement ranges. While there are some setups where this is a problem, there are others where I really want the carrier to keep its fighters close.
Glitched Sensor Array & Faulty Power Grid = Almost always a no. Some ships can deal with one or the other of these (SO variants tend to not care, for example), but as a general rule I won't accept either of these.