I came across what they call an "editable water bottle", but right as I dismissed the usefulness of it, another application for it occurred to me.
http://www.fastcoexist.com/3028012/this ... he-plastic
The immediate problem, however, is obvious: durability. The apparent lack of durability on the membrane looks to result in a projectile that won't be very aerodynamic. Special sabots would have to be designed, fired out of smaller launchers to make this work, and smaller projectiles result in less water. However, this may be even safer than water balloons already are, and don't have any environmental/disposal concerns. Unfortunately, having sabots would cancel out that benefit.
There are alternatives to this as well. http://www.wikipearl.com/ If the wikipearl is durable enough to maintain shape and stay in hard containers, yet brittle enough to break on contact, it could be a viable shell for containing water.
Of course, any of these probably have to be homemade. Having them pre-filled with water and buying them from a store would probably cost too much and not sell well. Mixing them the night before a war may be the only way to really make use of them. More research is needed, however, and something like the WikiPearl (and not like the "edible water bottle") is needed for durability and aerodynamics, but I can't yet find any information on how these are made. For something with the name "Wiki" in it, they seem awfully secretive.