I used to assemble and repair PC boards at one of my previous jobs, and I can tell you that it is perfectly safe to wash boards in water. In fact, durint manufacturing, right after the components are soldered on, the next step is to wash in warm water (and sometimes a special soap) to get the solder flux off. And if a customer sent in a dirty board for service, sometimes a hand-wash with 409 was the best thing to do!
But, nothing safe is foolproof, so if you are immersing board in water, take care of a few things:
-Remove all power. File this under 'duh'. If your motherboard has a removable lithium battery for the clock/cmos, remove it. (The soldered-on nicd batteries should be fine. Its more of a practical reason to not get water trapped in the connector under the battery.
-Not all components are water proof: Some parts came with a wrapper, that after soldering and washing the board, you peel off. This is mostly components like potentiometers which have moving parts, or piezeo buzzers that have a little hole. If a part has a hole in it, tape over it!
-If parts are in sockets, remove them prior to washing.
-After washing a board, don't let it air dry. Shake it off, then use a hair drier. Used compressed air to get all the water out of connectors and sockets. And make sure its totally dry before trying to turn it back on!
Now go clean your filthy electronics! 😀