By placing your glasses upside down, you expose the rim of the glass to any dust that's accumulated on the surface of the shelf, which is going to be more dust than can accumulate inside the glass, unless you are dusting your shelves as often as you are washing the glasses.
Top is how my finger looks after running it along the inside of a glass that was face up; bottom is how my finger looks after running it along the top of the shelf that glass is sitting on. Haven't dusted that shelf since I moved in 3 months ago. The glass has been sitting on the shelf since it was last washed about 2 months ago.
The amount of dust on the rim of a face-down glass would be insignificant, but the face-up glass is probably negligibly cleaner.