Look up the traveling salesman problem, computers, to determine the best route, would check every single possible route between all the of the selected locations. There are commonly used algorithms to speed up the process that result in less than ideal pathing to each location but this sort of problem is an exceedingly complex and heavily studied real world issue. Personally I am surprised that we can plot as far as we can in the time it takes, put multiple destination in and it becomes a big issue.
Now there are ways to simplify it by using the human brain, simply by having the player select the order in which to visit each location, and that will help with long trips where the to be visted locations are in an easily discernable order of some sort, so basically plotting to each location as if it were a seperate route plot, but just throwing star names in and expecting the computer to plot the route won't work, it has no way to determine which is the further site without actually working it out first, so there would still be a fair amount of manual work in plotting a multiple location route. This becomes an issue where players are using it to try and plot a many node trade route with the shortest possible travel time and distance.
When I did a bit of trading it did seem to me it would be an advantage to plot a circular route where the end station and the beginning station were the same so you could maximise profits, but as an explorer now I sidestep my plotted route so often and manually need to plot so much that it would be a big advantage. This sort of thing would be much more useful to traders I think.