The maps mark only the locations of systems that are:
A) known
B) inhabited
C) affiliated
There are plenty more systems in the IS other than the ones shown on the maps.
"Inhabited" is defined kind of loosely, too. Planets with extremely small populations, non-permanent habitation, etc. are left off the map unless they're otherwise notable. There are a lot of systems out there that have a few dozen people living in them, but they're not considered self-perpetuating colonies. Research outposts, mining expeditions, or just plain old hobo camps.
And then you have planets that were rendered post-apocalyptic wastes by the Succession Wars, that still have native populations but don't participate in the culture of the Inner Sphere at large. A few hundred or thousand survivors clinging to life in the ruins, with no access to space travel or communications. The planet itself is so badly damaged that it has no further value for scavengers, so no one goes there, so there's no point in showing it on the map.