Yes I know what vacuuming does. I do this type of work for a living except on systems that hold 20+ pounds of refrigerant and get way colder then the ac systems in our trucks. What i'm saying is i highly doubt that you got all the water out in a couple of hours. You might and you might not i'm not going to argue with you on it. Its you truck do what you want. I wouldn't take a chance of destroying a new compressor due to having used water to flush something when there is a product that works far superior and is designed for a specific purpose.If you put a vacuum pump on it the water evaporates and gets sucked out. That's a big reason why you use a vacuum pump. Even if you aren't necessarily flushing your system, oil won't evaporate in a vacuum, and any condensation contaminating the oil boils out and is expelled.
EDIT: It occurs to me you might not realize I am talking about flushing out the evaporator, not the entire system. Yes, trying to flush out the accumulator with water is a bad idea.