If the drones can appear anytime, [not necessarily anywhere, there may be specific areas of space where they can and cannot spawn], this has an interesting effect for miners and haulers.
I think it's good, and i think there will be people that absolutely despise it.
If hostile NPCs can (and semi-frequently do) appear... you finally have a reason to make a combat capable mining ship!
I was trying to avoid introducing "roving packs of hostile rogue drones" in this thread specifically, but I think it's a natural evolution of the idea down the line. As it's laid out right now, the three starter rogue drones (derelict, caravan, complex) are activities you seek out rather than them seeking you out. That said, I think it'd be really interesting if there were especially dangerous regions of space far from origins and gates that did have active and hostile opposition, and for which you did need an armed and armored mining/salvage ship even if you aren't worried about players. It's probably out of scope of this specific suggestion thread though, and I want to focus on things that I believe are achievable first by repurposing Starbase's existing game systems before adding lots of new ones.
I agree with your later points that right now arming and armoring a mining ship is usually a waste of effort since you're still pretty unlikely to win. With dev-designed rogue drones as adversaries rather than players though, the difficulty can be calibrated more precisely to make those scales balance out a bit better.