The Nihilanth, I think, led the Controllers (and therefore the Vortigaunts) to Xen, where they hid from the Combine. I understand they were repeatedly defeated by the Combine elsewhere and wound up hiding in Xen specifically because the Combine could not get them there.
The Nihilanth is a modified controller, augmented to give him teleportation and other powers needed to help fight/evade the Combine (hence the stitches and metal/flesh fusion). I think.
The stitches suggests that it may have been experimented on possibly by the combine. I would imagine that before he fled to Xen he may have held a title similar to Breen.
Think about a planet full of his race, them being the dominiant planet, ruling over the tribesmen-like vortigaunts.
Combine comes and invades the planet, much like Earth. Some stuff happens and Nihilanth's race is gone, him being the last, and he is horribly mutiliated by the combine due to the experiments done on him to synth him.
Now, my point is: Do you think the combine has an army of Nihilanth Synths, like he has an army of human synths on Earth? We'll probably not meet any, even if theres, say, 10 million of them. The Combine Empire spreads among entire galaxies, their powers must be stretched horribly thin, thus must be why they use mainly the creatures they synth from that planet, once they take over with the initial assault. This would make a good answer as to why we have not seen a vortigaunt synth yet (because they were not the dominant species, and the combine went for Nihilanth(s)).
PS: Yes, I use the word Nihilanth to address the whole race.
I agree with Eejit. I've always seen Nihilanth as being controlled by the controllers (shackles, etc) even if Laidlaw described the controllers as Nihily's "support network".