Circa 2010, I decided that the navigation in Freelancer was severely lacking... so I built a nav computer, and entered systems in it as I discovered them. Enter your current system and the destination system, et voila! Shortest route.
It appears to use a basic breadth-first search. Also, judging by the empty sections in the fl_sys.py file, this might not be a complete map.
python fl_nav.py
OR
chmod +x fl_nav.py
./fl_nav.py