The fundamental issue comes down to "even though armors actually lower damage", namely a side effect of that. With armor reducing damage, nanobots are proportionally more effective - if you're shot for 50 damage and nanobots heal 200, one bot heals four shots. If armor reduces that to 20, however, one nanobot heals ten shots.
You could sort it out by also merging bots with hull. This also reduces the risk of instakills further, whether that's good or bad is apparently up for debate.