The reason for why large formations of ships don't "come at them from below/above" is probably because it would be dang hard to coordinate, moving a large formation of ships like that would take way too long, and in the meantime the enemy can easily attack the flank or retreat.
By the time you actually get "above" the enemy would have been waiting in it's new formation for several hours/days
Now that I think about it, Gunbuster 1 had some nifty "realistic" things and a whole lot of not realistic things of course, maybe not the kind of animé one would be looking for "space warfare" but it's worth a watch anyways.
