Yes this is pretty annoying. In most cases, I just have a request for more cargo pods in all my ships.
The only REALLY annoying case is your first science drop platform that everyone builds. That design drops 1/2 at a time constantly and eats up cargo pods. My solution was too dumb for words and not reasonable (I made a science ship that flys to vulcansus until it has enough science before returning to navis airspace).
Adding GUI controls is a bit beyond my ability to mod. If someone in the community knew how to do that, and add some control logic, IE only drop if you have at least X of a given unit, I'd be happy to accept pull requests through github.