When you use a formerly unused JP the game takes a random number from the possible system IDs (100 or 50 for your example) and creates the link. if the target system doesn't exist, it will be generated. If it already exists and has unused JPs, one will be randomly used. If no free JPs exist, a new one will be generated.
With your galaxy size, unless you run out of JPs, you will probably end with a very densely connected galaxy, simply because there are not that many systems to begin with.