I can't speak to Known Stars, but on Random Stars there is a definite issue with having no connections to existing systems (loops), or dead-ends. To demonstrate, I loaded up a fresh copy of 2.1.1, started a new game with the only alteration to system generation being to set it to Random Stars. I then SM explored 150 systems. Attached is the screenshot of what the system map looked like. As you can see, there are no loops and there are no dead-ends.
In 150 systems, this is... highly improbable, in the absence of some kind of system generation and selection issue.
EDIT: In the image, System#891 appears to be a dead-end; this is merely a display issue due to it being the final system I SM explored and the galaxy map not updating to show it. I checked and it does indeed have an unexplored jump point.
Assuming 1000 stars, with Local Chance at 50 and Local Spread at 15, there is a 50% chance that the JP will connect to a system number within 15 of the start system. That doesn't mean it will connect to an existing system - just to that number. It will only connect to a system if one is already occupying that system number slot.
There are also some restrictions on connections. A jump point can't connect to a system if the two systems are already connected - which affects exploration from both systems. Also, the last unlinked jump point can't connect to an existing system.
So 50% of the time, any system from 1-1000 will be chosen. Early on, that means a very low chance of connection. The other 50% of the time, it will be a system within a 30-system-number range centered on the existing system, but again unless those numbers contain existing systems there won't be a connection. Of course, every time you don't get a local chance hit, you move to a new area with none of the 30 local spread slots filled in. As you are moving around 50% of the time, most of the time you are in fairly barren local spreads. In fact, the second system within any local spread won't connect to the first one - because the connection already exists, so you are more likely to be in a new local spread before the current one can connect. Plus every time you hit a new system, the 'local spread' moves to include new unexplored slots. Even after 150 systems, you have only filled in 15% of the total slots, so the result you have is unlikely but possible.
For known systems, there is a fixed chance of finding a connection, but in random systems the total number of systems plays a large part. With 1000 systems, the chance of randomly hitting one of the filled-in slots is pretty low.
I just ran a similar experiment to yours, tracking all the generated system numbers and stepping through the code. I didn't find any links in 45 systems. Changed to 100% local chance (so I am not jumping around the whole 1000 systems) and hit a connection within 4 attempts.