I agree that NPC crew must exist. I also understand performance wise that they could potentially be a problem. I also think that both automated systems and crew should be available. On the performance aka no lag side, your crew should be mostly for show. They are loaded only in areas where they would be visible. They are not really real however. As the ship takes damage, I would think crew would be sucked into space, so heavily damaged areas would not have crew every where, they would be gone and you would never see them.
This is how I envision the game to work with crew vs AI automation. Building a ship would require you to make an important decision, automated with little to no crew, or no automation and all crew. Gameplay wise would be the same in regards to ship control and operation. You would get onboard, go to some control station or bridge, and either command the ship where to go or pilot it directly. Now the ship in direct control is not being flown by you, it would technically be the crew or AI interpreting your actions. If there is no crew or automated system, then the ship would not respond, and you would need to access the flight controls directly.
A fully automated ship has advantages over a manned ship. The ship would have no need for more living quarters than what is needed for the captain. One bedroom and minimal life support. This reduces ship size as you don't need crew accommodations. All ship commands and direct input are fast. The downside? Damaged areas and systems could disable important AI systems such as self repair, or piloting controls. The ship might no longer go when you say to our give direct input to throttle up. Now you must dispatch perhaps separate drones to fix them out go do it yourself. Heat generation would be much higher with all the AI systems controlling the ship and you would be more vulnerable to virus, hacking, pulsars, emp, and more. Enemy boarders might have to have automated defenses, but not if they are down. Lastly, the extra wiring and added material cost to build these more expensive and fancy systems.
A crewed ship would be similar but with many differences. Advantages are less heat output, simpler command consoles which might resist emp and such better, onboard defense, multitasking by reusing crew at different stations, more consoles while increasing material cost makes it more difficult to disable individual systems being more spread out, and of course misusing your crew and making them say funny things and having to slap your officers in the gave with a leather glove. Disadvantages. Virus, illness, larger ships on average due to crew Accommodation's, higher life support requirements, passages needed to access entirety of ship, supplies for crew, shower response time for all systems, and of course crew talking back needing a smack on the bottom.
I would build a ship that might perhaps use a bit of both. I might forgo a helmsmen in favor of an AI control core so that I know the ship will move and respond faster with greater reliability. But perhaps use a crew member to manage navigation and weapons.
I believe that both can work fine together and allow for both micromanaging and general orders. So you could focus wherever you want. You want redshirt 53 on helm and 56 on weapons, go for it. Don't care, somebody just auto man's it.
I think this will all work just fine. Perhaps PvP might have rules or have settings for how many of what you can have on a ship. That way PvP can be the side game mode and pve can be the main game as intended. I would expect that more than a dozen or so ships plus fighters would be very chaotic so there really is no point to having hundreds of ships in a fight, or rather capital ships. Hell even sins of a solar empire, a 4x RTS game limited capital ships to around a dozen per team with a max of 8 players. A giant battle is nothing more than many smaller fights going on in unison, and while cool, is not better than watching a few ships get ripped apart up close and drifting through the debris lining for treasures and trinkets.