Bear in mind that SHIELD and HYDRA are selectively recruiting (they're a biased sample) - so having a few inHumans doesn't mean the number in the population is high.
But to be fair, after further consideration, maybe even inhumans without powers have some trait that we don't know about much more frequently than the general population - e.g., a psychological predisposition to be in law enforcement, or to be members of secret organizations, etc. -, which would explain the high numbers, so you make a fair point. It's still the case that 3 inhumans in a small group of characters is evidence of a higher percentage in the general population than if, say, there were no inhumans among known SHIELD or HYDRA agents, but it's weak evidence.
On the other hand, that raises another issue: how many agents of SHIELD and HYDRA are inhumans, and how is SHIELD dealing with it?
I mean, I would expect that HYDRA - just as the ATCU is doing, sponsored by HYDRA- would offer terrigen-laced fish oil to all of its agents - at least the part of HYDRA that knows about it, which includes Malick's HYDRA, and now probably also Ward's.
That would allow them to increase their numbers of powered agents.
Yet, Coulson seems bent on finding a cure, calling it an "infection", and not trying to expose anyone to the mist.
The result?
One would expect that HYDRA would get a much bigger and more powerful team of inhumans than SHIELD.
Granted, the sample is still small, so it's not very strong evidence. But it's something.
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