They're not really "missing", you just can't get there except by travelling aboard the Osiris during the SP campaign. You could open up some jumps with a mod, I suppose, but they'd probably just be dead systems to cruise around in, with nothing going on there.

I made a jump hole into the Omicron Minor system and was able to get back in after the sp missions. Toledo was still intact and all services functional.I was also able to use the Alien Jump Gate located in this system to Omicron Major where I encountered waves of nomad fighters. Then back through the A Gate to Omicron Minor and when I try to dock with the jumphole I made to get back to where I started, the game crashes. I wish I could fix this but I can't figure out why this happens. I'm thinking the nav map might have something to do with it. Getting back in is easy, has anyone figured how to get back out without crashing the game?

What you could do is you could modify the ini's to include a Nomad Lair and a jumphole to Omicron Minor in the Omicron Beta system, cant be in the center like in the fake omicron beta though, theres a base there and some wrecks.

"It is said that revenge is a dish best served cold, it is very cold in space."
~Khan, Star Trek II: The Wrath of Khan

While your traveling between manhattan and the colorado jump gate type in windowsrules really fast and you will suddenly come out of hyperspace and magically be in the omicron minor system. But never forget that drunk ewoks are known to lie all the time...

"You can pick your friends and you can pick your nose, but you cant pick your friend's nose."

Han Solo - "What an incredible new smell you've discovered [!"

I made a jumphole in the unknown system next to Omicron Gamma and connected it to Omicron Minor. This will get you there and back

Do you think you could give me those files, I'd really like to visit all those systems (Omicron Minor and Major and the Nomad one!!) but I hace no idea how to make my own jump holes. That'd be great!!!

The Space Raven.