We returned last week, and never were asked to empty our water bottles. We always went to 2 parks a day for 5 days, and sometimes we went through security 3 times with all the coming and going.
I would have been very upset if they had done that because we bought bottled water. I imagine your local parks may do that to prevent teenagers from putting vodka, etc., into water bottles. That's not a big conern at Disney World.