This is a really neat idea. As others have noted, balance is off a bit - some of these are definitely more valuable than others - but it's still a really neat idea. Kudos.
My assessments:
Hegemonic Plating: Simple and to the point. Not a really significant bonus, but nothing to sneer at either.
League Leadership: This one's pretty powerful; at least personally, I rarely have the OP available to put expanded deck crews on my carriers, so I'd be getting the full bonus more often than not. On the flip side, the Persean League is pretty boring as a faction, so giving them an exciting and potent crew bonus is, imo, actually, a good idea.
Sindrian Endurance: An interesting idea, but... not actually that useful, at least for my playstyle. I'd probably combine this with something like a 10% reduction to ship maintenance supply cost.
Blessing of Ludd: This one is, um... weird? The effect seems fairly reasonable, but the flavor-text could use a re-write. Something like "Eschewing automated tracking systems, each missile is individually remote-guided by Luddic gunnery crews."
Tri-Tech Assistant: 100% useless bonus. There are several sources for auto-aim accuracy bonuses (High CR, gunnery implants skill), and they already add up to more than actually has any effect. That said, I'm not sure what would be a good replacement here. Maybe a 5% reduction to shield / phase cloak maintenance flux costs?
The Path: One of the more powerful options. On the other hand... you've got a commission from the Luddic Path. That probably balances out.
Pirate Handiworks: Powerful but situational. Though, again, if you're allied this closely with the pirates... well, not only does that mean you're more likely to be in a situation where this matters, it also means you do need all the help you can get.
Hm. Yeah, okay, so that's just Sindrian Endurance and Tri-Tech Assistant that I think need work.
Question: Do these bonuses apply to ships from the given faction, or just player ships when commissioned?
Edit: It's been pointed out to me that the above question is unclear. What I meant to ask is if this gets applied to fleets controlled by the given faction, or just the player's fleets.