The potential damage output for drones displayed in the Fitting Window only takes into account drones located in the drone bay. Once a drone is launched into space its potential damage output will not contribute to the one displayed in the Fitting Window.
Furthermore the potential damage output will be calculated based upon the optimal combination of drones in a players drone bay and limited by the maximum amount of drones that they can use at one time. If for instance a player was able to use five drones simultaneously and had 5 Hammerhead and 5 Hobgoblin located in his ships drone bay then the potential damage output would be calculated based on the 5 Hammerhead drones. If those five Hammerhead drones were launched into space then the new damage output would be based upon the 5 Hobgoblin.