I think this will become a non-issue once more exploration content is introduced. Fighting domain drones is only so boring because domain probes are one of the few things you can find during exploration, so you fight them all the time. Trying to upgrade them to a level where they can still challenge a high level player fleet just makes them unbelievable in the role of "ancient relics".
Just because you will have more things to blow up doesn't mean the Domain Drones being boring to fight will change.
And you can actually justify the 'upgrading' or 'waking up' process.
During exploration period and after it, Domain Drones weren't attacked often, so they didn't have to develop countermeasures, but Domain's engineers and scientists expected this to happen at some point.
So they added either a package with instructions what to do in case this scenario happens or they added blocked off pieces of code which are enabled when this scenario happens.
Aforementioned measures can contain special blueprints which are more suited to fighting ships used by the Domain, alongside special weapon packages which are easy and cheap to make, but are dangerous enough to make sure enemy won't come out unscathed.
And about the Mothership - they were mobile in the past, they did have to get here, to the Persean Sector, somehow. They fell into disrepair during that 'sleep' process. So Drones fixing the Motherships in face of a threat which targets them makes sense.
Mission has to be carried out.