They are the same except that "located along" implies that more than one of something are set in a line. That is, each one is separately located next to something else.
For example, if I say "The cities are located along the river" it implies that they are lined up, each near the river, and if you travel up the river you will come to one city, then the next, then the next.
If I say "The cities are beside the river" it implies only that at least one city is actually beside the river. The other city or cities could simply be close to the first one, and therefore grouped with it, or perhaps one city is on one side of the river, and one is on the other side. Either way, if you were to travel up the river you may only encounter one city, or you might see more than one at a time.