There's a little bit of Ted Backman (male_02.mdl) in all of us.
Interesting proposition! Although I may revise your theory in a slight manner:
It's my belief that the Headcrab species were modified by the Combine following the events of the 7-Hour-War. Headcrabs as they existed at the Black Mesa incident were the closest to their "natural" forms we have on record, while the Earth-dwelling variations seen since seem to have evolved to suit their new environment, either through genetic modification, or by natural means.
I'm partial to the belief that genetic manipulation is at play here - the Combine have demonstrated their weaponisation of the species through mortar shells. Reason leads me to believe that their synth-creation practices extended to the modification of the Headcrab species in slight ways, producing the differences we've seen in their appearance over time.
I don't see the point in genetically modifying headcrabs. In the sense, why is the Combine? What would then, after the bombing, fight the territory with uncontrolled monsters of different versions? So most likely this is the result of the natural evolution of headcrabs.
I like this a lot, I have a different theory regarding the Gonome though. Zombies probably just need to have access to a lot of food to become a Gonome.
We saw Gonomes in Black Mesa because there were corpses everywhere, we don't encounter any Gonomes in HL2 because there aren't many corpses around. Even in Ravenholm there weren't many human corpses since almost everyone was Zombified by the Headcrabs that were shelled in. And the HL2 Zombies are just a redesign of the HL1 Zombies, I don't think they're actually different at all in lore.
The math we deserve.