Not intended. Spilling is a last resort so cargo is never deleted outright, but a drone should never have been sent to a depot with no room for what was already on its way back. The check asked whether there was any free space at all rather than enough of it, so a nearly full buffer still launched the whole flight.
Your suggestion is what it does now. From 1.2.1 the depot counts free space in items, subtracts what is already in flight, and holds the drones instead, with a note on screen saying why. 1.3.2 closed a second route to the same pile: a nearly full pallet accepted a full load and the remainder came back to a depot that had filled up meanwhile.
Both are in 1.4.0, which is up now. Thanks for the report - and for asking whether it was deliberate rather than assuming.