I've got to agree that we need more spaces for bots. Maybe leave the original six slots for our personal bots and then have a storage room upgrade with X slots for bots we are repairing or selling. Have the bots in those slots unable to be assigned jobs, meaning the only job xp they get is from direct training. That way players aren't just filling up the warehouse with bedroom toys, leveling them all at once and then selling them off to the brothel en-masse.
Second, I'd suggest making the player's home more up-gradable in general. Amenities that reduce stability decay for bots, better tools to improve our work, possibly manufacturing capabilities.
Third, you've got stats underutilized. Combat does nothing. You track familiarity for individual parts and bot types, use that. Autonomy is basically limited to how many jobs a bot can have, that's wasting it. For example, you could make it so that bots will do there jobs even if your not actively there. Maybe set a system to flag parts for sale then have a chance that you can return from a scavenging run to find your clerk has sold a bunch of parts for you. Profit determined by the social skill. Use that part familiarity tracking to have bots take care of basic maintenance for you, for example if you have D rank familiarity with a Nova power core then a bot can repair it up to 60% by themselves. If its B rank then they can bring it to 80% and fix minor defects. If it's S rank then they can fix anything that is fixable. Use the bots autonomy and mechanic/engineering skill to determine if they fix something and how much they get done.
My fourth and final(for now) suggestion, more uses for the bots in general. Set it up to send bots out on errands, say you need a powercore maybe have a tech bot go scavenging for you, or have a clerk go out and check the flea markets. If I were in the MC's shoes, I'd eventually be running at least 6 bots 2 each combat, tech, and clerk. One clerk would run my counter, one combat would handle my shops security, and one tech would handle the basic repair stuff, letting me focus on repair contracts and more important repairs. The other three would be sent out to find parts. the tech for scavenging, the clerk for haggling, and the combat playing bodyguard for both.
I get that some of this would be a cast iron bitch to code, and worse to balance, but I think they would be pretty good improvements for rewarding longer term players.