The SRV doesn't have an AFMU. But no, the AFMU has to be manually triggered, and it turns off whatever you're trying to fix while it works on it.Does the AFM work in the background or do you have to completely shut down your ship first? Every time I rebooted the same NPC pirates kept attacking me.
Not sure what it has to do with pirates, though. I guess you were hoping it would repair in the background after an attack? Unfortunately, it will not. You have to stop somewhere and fiddle with it. I've only ever messed with one once, on a long exploration trip. It worked, but I decided I didn't need it much and never took one with me again