To answer your question, yes, they are more than just bot-feeders. When ships have their shields down, the nanotool on the Repair ship will slowly(quickly) repair the main hull of the ship. This repair was used on a certain battleship named Harmony and it took it from 7% hull back to 100%.
Other than that, the Repair ship doesn't have much use. Bring one to a massive battle for a last stand kind of thing and it might even turn the tides.
