1. I get that a lot too. At least they're trying to be helpful; from their perspective it would be embarrassing if they gave someone obviously foreign the Japanese menu. Most people's exposure to westerners here starts and ends with English teachers, so I would forgive them for this one.

for 2 and 3, I think it is because they are actually surprised; there are a lot of (Japanese) people who don't like natto or umeboshi either, and kanji is something they spend hours per week studying for 10 years to be literate in.

4 is a hard one. They assume that a foreigner obviously can't speak Japanese. It can be super annoying.