Do brass ball valves have to be oriented with the flow of water?
If a valve has directionality, it will almost universally be cast as an arrow in of the body, as seen in this globe (aka stop) valve:





I've never seen a ball valve that is directional. If you look inside, you'll see the guts of it are symmetrical.



I would say the general rules of thumb for this are:


If you can even change the handle direction, be sure that off is perpendicular to the pipe.
If clearance or safety is an issue, then install it in the way that works or is safest. 


For example, if it's sticking out when it's off and likely for someone to accidentally bump into or get caught on it, then install it the other way so that doesn't happen. 

If clearance and safety are non-issues, and there are other valves present, then follow the convention of existing valves. 


If you have pipes that flow in opposite directions it's very handy to ensure the valves indicate this. 

If there's no existing valves, and no clearance issue, then the most common convention is to have the handle point in the direction of flow. 


There are probably regional and/or industry-specific variations to this, but as far as North American potable water goes, this is it.