I think it started with nearly_naked_apron, but other nearly_naked_* tags have been created without prior discussion after that.
In general, a naked_* tag means that a character is basically naked, but wears a single piece of clothing which can lead to them not qualifying for nude anymore. Otherwise, we'd simply tag them all nude + *. (Exceptions are being naked and covered/wrapped in ribbons, bandages, chocolate, which also use the tag name naked_*)
(BTW, naked_scarf is also pointless, since it is just nude scarf)
Now, to the nearly_naked_* tags.
For example, take nearly_naked_shirt. The condition is wearing a shirt and underwear. How is this any different from the no_pants tag?
Or nearly_naked_cape. Which is cape bikini or cape underwear_only