The word barefoot is an adjective and is used to say that someone isn’t wearing any kind of footwear. (i.e., no shoes, socks, sandals, etc.) It decribes an ordinary or general state/condition.
Naked foot is two words: an adjective (meaning bare) describing a noun (foot). (I’m sure you must know that. ;))
It refers to only one foot and is not a “standard” or “everyday” collocation. So, you’re right: It’s unusual. However, there’s nothing wrong with using the two words together — particularly if you want to talk about something other than the fact that someone simply isn’t wearing a shoe on a foot. For example, in a situation where you are looking closely at or examining someone’s foot.
Regarding your sentence, what about this:
[i]I do not think the second one is used frequently - or at all, for that matter!