Number of systems is not important. Concept behind all those new systems is rather simple.
Populated systems are explored, allright. But what is in between of them? Empty space? Logically there are more stars and more systems, unexplored and lacking any population or viable resources.
Moreover, did you note where clan systems are located? Most of them are connected to 2 systems: one 'home' system of original faction, second empty system that is not connected to any other populated ones. There's one obvious way into each of those systems, and one hidden way that takes much longer, but may catch system defenders unprepared.
Next. About player-generated content. This applies both to clan systems and any other systems that you may like to edit. There will be special procedure about system submission that I'll post later, along with brief instructions on how to edit systems reliably in FL Explorer. Anyone who's enough careful and attentive will be able to 'populate' those systems. And I will add certain objects there too, surely.
Hiding systems? Well, many paths are hidden quite well as they are now, and I see no reason to restrict access for players. Besides, restricting isn't that easy.