It's clear one's got the hints (9)
I believe the answer is:
overtones
'the hints' is the definition.
(I've seen this in another clue)
'it's clear one's' is the wordplay.
'it's clear' becomes 'overt' (both can mean apparent or obvious).
'overt'+'ones'='OVERTONES'
'got' acts as a link.
(Other definitions for overtones that I've seen before include "subtle innuendoes" , "added nuances" , "Upper partials" , "Subtle implications" .)