How should glasses/cups be oriented in storage?
If the glasses are at all damp, it may make sense to store them up-side-down. In bars and restaurants, you often see plastic mesh like this:



That webbing lines trays, shelves and the area beside the sink for drying dishes. The mesh keeps the dishes or glasses, which may still be damp, from actually touching the surface they're sitting on. In the case of glasses, it also keeps the glasses from forming a seal to the surface beneath. That mesh often gets cleaned, as does the surface under them. In that case, it makes sense to store glasses up-side-down.

Do you have mesh lining your cabinet? Are the cabinet shelves wiped down regularly?

If not, it is far more sanitary to store your glasses right-side-up, and to be sure that they are dry before they are put away.