I kinda wish they redid the old vortigaunt sounds. In the first one I thought of them just as weird, creepy aliens but all I think of when I kill them now is all that praise they gave the freeman (and of the black guy doing their voices). Almost makes me feel like in HL2 they shouldn't be praising him so much.
They're enslaved though. Notice how they're all wearing these green metal shackles? And how the Vortigaunts in HL2 don't, except that one by the trainstation who is sweeping the platform floor while the Combine soldiers watch? Yeah.
Hm, Nihilanth's chamber is actually pretty humble for the leader of Xen. Just a huge cave with spikes.
Nihilanth is enslaved just like the Vorts; he wears metal shackles, propped up on a floating device and trapped in a chamber without escape. Come to think of it, the surgery marks on his belly, his unnatural anatomy and the metal parts attached to him makes him seem like a synth (bio-engineered creature filled with machinery). The Combine is nose-deep into everything relating to the resonance cascade, they just aren't named.
Edited:
Also regarding the Vortigaunts praising you, they do have one rather interesting line that goes something like "We cannot forget those whose cords you severed. Forgiveness is not ours to bestow". While you slaughtered them by the hundreds while they were enslaved, you ended up liberating their entire race in the end by killing Nihilanth, so them respecting you makes some sense after all.