I didn't read the entire thread, so forgive me if these questions have been asked:
The quick answer is we do not 'know' any of the answers. The people who have contributed to this thread are not the people who are doing the final design. It is a virtual certainty that much of what has been discussed in this thread will find it's way into the game, but exactly what, and what the particulars will be is right now a complete unknown. However as someone who contributed much to this thread and has followed it obsessively, I can give you my best guess as to the answers.
1) Are crew bonuses a +X% of ship capacity, or a static +X regardless of ship modules? Here are some scenarios:
Small Ship, 1 wepon computer and 1 weapon module, deals 10 dps
Large ship, 1 weapon computer and 1,000 weapon modules, deals 750 dps
They will almost certainly be a bonus to the ship capacity, but the quantity of bonus will be dependant upon the quantity of crew. A large weapon will require more crew to get the full bonus. A ship with a tiny weapon may get a 100% effectiveness bonus to it's damage rating (or whatever), but that bonus would be on the small weapon, doubling it's effect. If the weapon were ten times bigger but had the same number of crew, it would only get a 10% bonus for the crew. The idea is to make having crew and very specifically the mass/space devoted to supporting the crew, slightly more effective than devoting everything to nothing but systems.
2) If I have a ship with a weapon computer but no weapon modules, does the member gain experience? What if that same computer had 10 modules, would they gain XP faster? What if that same computer had 1,000 modules?
Total unknown at this point. I expect the weapon computer would have to be serviceable, actually attached to some sort of weapon. Whatever is decided upon when it first goes live will almost certainly get tweaked as we see how people game the system. If it were me I would tie the XP gain to weapon size but cap it at something like 1000 modules for a weapon. I suspect that would reduce the abusability the best.
3) If I unassign a crew member from their station, do I still have to pay them?
We have no indication as to the support costs or what they would be paid from. I have campaigned for paying them out of faction points. If they are unassigned, they would still be a faction point drain, but you would retain any XP growth they had gained up to that point. If you dismiss them so as to save faction points, you would loose any XP gain, they would not be rehireable.
4) Is there a cap on how high a level the crew member can be, or how much of a bonus they will give? Do they age/die/retire after a time, or would it be possible to have a 5,000 star commander?
I expect there will be a cap, as that is typically how XP systems get implemented. If I were programming it myself however, I would have a logarithmically increasing cost for the next bonus level and no cap. It would as a result however become progressively harder and harder for them to improve. I expect they will be immortal unless killed in combat, if for no other reason than to reduce micromanagement.
5) Should there be a limit on how many crew members can be on a ship at one time? If my ship is 1,000 blocks mass but has 300 computers, is that legitimate? How would we control that other than pay?
The practical limit will be that each crew member will require a certain amount of crew space, likely their own controller block, and probably a few other blocks including their work station. If you want to add 300 computers attached to 300 single weapon blocks and try to fly that around with the quite large crew space that would entail in tow, I see no game reason why you couldn't. Better hope the pirates on your server are pushovers though. Plus, they wouldn't gain much XP controlling such a small system.
6) Do crew members gain the same XP if I am fighting a ship vs just being in a hostile sector? Couldn't I just cloak, park, step away from my computer, and rack up XP? Or form an 'alliance' with a fake enemy to use each other's 'hostile sectors' to gain XP for our crews?
Combat would return the most XP by far. Simply flying about might gain something, but it would be a relative trickle, and only then if in hostile space. NPC factions would probably have to be programmed to set off their scanners every once in a while to keep such training ships honest.
7) How do I hire crew? How do I fire them? Can I trade/sell them to another pilot/player?
We have no indication yet how this will be handled. It will probably be a simple menu at a trade station and a crew person will poof into existence for you. Firing them would also likely just be a menu option in a relevant screen. Trading/selling them is an interesting option. I have no idea if that will be a feature when first released. Probably not, but it might be added later.