See, I saw everybody just taking that bit in stride, and I was wondering if I’d missed a new piece of lore.
Yes, Nihilanth was a human on growth hormones, but the experiments went out of control as he grew too large for Combine to have a sufficient amount of food for him, so they decided to get rid of him instead. Poor guy had to escape and feed on Vortigaunts instead. Source: my arse.
One word: controllers. They’re probably the same or a cousin species to Nihilanth and they’re not human.
Anyway, back to the topic of the Vort language, folks. 
The beta voices for the Vortigaunts actually sound much closer to the HL1 versions, but the trouble with that is they do not sound friendly, they sound scratchy and prickly. To make them seem like better allies, Valve probly retconned it and gave them a much smoother and warmer voice.
Maybe the slave collars affect their vocal cords (or whatever vorts have that makes them capable of speech) somewhat similar to what electrolarynxes do for humans.
There’s that scene in HL2 where they mention “flux shifting” or something as a method of communication that humans can’t detect. Maybe they were using that in HL1, and it took them time to adapt to speaking vocally.
But then in EP2, the Victory Mine Vort uses the HL2-voice even when apparently “flux-shifting”.
I call retcon.