They are still headshots, right? I think the perk system currently only counts headshots which kill the target. If you score a headshot on, say, a Fleshpound and it survives it doesn't count as a headshot.
In my opinion it should count. Not a huge deal, just a matter of consistency. If it's intended to not count those shots the description on the perk screen should be more detailed. Like, "remove this and that many heads".