It is pretty unusual to only do one head gasket on a V6, which has two. The reason is that the extra labor for two versus one isn't that much, so it always makes sense to do both gaskets at the same time, since you already have the motor apart.
As for whether is makes sense to do the entire motor rather than just the head gaskets, that really depends on your individual car. If the motor is in really bad shape, and you'd probably be looking at another big repair in the near future that a new engine would avoid, then it may make sense. It really depends on your car and your engine.