I really enjoy having NPC crew on many of my ships, but I have to admit the current limit does make sense from a balancing point of view.Drop the one NPC-driven SLF limit already. It no longer makes sense.
A GELID F fighter for example deals 45 DPS; that's more damage than 2 Large Gimballed Beam Lasers (and nearly as good as 2 Fixed ones). On a Krait Mk II for example it's like having 2 medium and 5 large hardpoints... but better if you have an Elite NPC crew member as they can stick to their target like glue and provide a distraction to other NPCs who will nearly always target the SLF first.
Now imagine having 2 Elite NPCs, dealing an additional 90 DPS, equal or better than having 4 extra large hardpoints on your ship. Does that sound balanced to you? Powerful certainly, but balanced?
An argument could be made perhaps for allowing a Class 7 Hangar to support 2 NPC crewed SLFs, as they're only available on Large ships which can't bring all their weapons to bear on a target, or maneuver particularly well, but maybe that would have to come with additional limitations to prevent them becoming too powerful.
All in all balance is a difficult thing to get right and I don't envy FDev the challenge. To be honest I'd much sooner have the NPC crew member actually sit in the cockpit (unless we have 2 human crew in the seats). I think that would add more life to the empty pit and create that little bit more immersion.