Instead of studding the gondola surface with UVC LEDs, you could encapsulate the gondola in its own small balloon made of cyclo-olefin again, and sterilise that with LEDs on the gondola shining through it. That way you might only need 4 or 6 LEDs, say. There could be one opening for the sampler.
The gondola within could be left "dirty" or could be extensively sterilised groundside. The trick throughout is to sterilise everything exposed to the air in flight - main balloon canopy, lines, gondola canopy - in flight! Hence the LEDs.
Any cyclo-olefin manufacturers out there?