a book store with a café

This is easy because the tags don’t overlap.

shop=books
amenity=cafe

a café by day and a wine bar by night

I saw something like this before, and they are usually two businesses with different names. I used two separated POIs (points) placed in the same building area to denote them. In this way, I can also put different names, opening_hours etc to the two POIs.

This is a longstanding issue that wheelmap knew and promised to solve.

Some info from the OSM talk mailing list.