Well, the cloaking is valuable if you keep it out of range of anything that it could fire on. This is why the cloaking scouts are needed, they have no guns and are purely for scouting. The scout starship is really meant to be more of a hard-to-kill mobile scanning station to go with your fleets. If it worked better as a pure scout, the true scouts would be pretty useless.
In fact, the cloaking ability was something that I just added recently for the scout starship, and the main reason I did that was so that it could sit at a planet without getting reamed by sniper fire.