On (1) oh my goodness, this is getting a little over the top now. There are just as likely to be germs on your stateroom door handle, on your in-room safe, on elevator buttons, on the stair hand rails, on the restaurant booth--all of which are "handled" just like the top cup. It is really getting far fetched to think someone would drop a cup on the floor and then replace it on top of the stack--if it falls on the floor, anyone would throw it away. Please don't throw away a handful of cups just to get one that you can be assured is pristine; it's so wasteful and you are not incrementally reducing your exposure to germs above and beyond all the other things that people are touching day after day.
On (2), I'm sure some people who improperly "save" seats when nobody is coming to claim them. But bathrooms are actually packed right before a movie, because nobody wants to have to leave in the middle of the movie to go. Not to mention that a lot of the saved seats are for people getting popcorn.