Etymology holds the answers (usually!)

The prefix sub- is derived from 14th-century Latin, meaning "under, or somewhat"

For instance, we still see this when using "sub-par" or "sub-zero", and in "subliminal".

-tle has been condensed, dating back to -tilis, from -tela, meaning "web, net, fabric". This is a derivative of "texere" meaning "to weave" or "to construct".

In the 13th century, Subtle was a surname, meaning "sophisticated, ingenius, or refined".

Essentially subtle has boiled down to "doing something" (texere) "slightly" (sub-).

Etymology is the best!