Could be cleaner though there's nothing in it (6)
I believe the answer is:
vacuum
'there's nothing in it' is the definition.
(I've seen this before)
'could be cleaner' is the wordplay.
I cannot quite understand how this works, but
'cleaner' could be 'vac' (I've seen this before) and 'vac' is located in the answer.
This may be the basis of clue (or it may be nonsense).
'though' acts as a link.
Can you help me to learn more?
(Other definitions for vacuum that I've seen before include "A region empty of matter" , "Emptiness" , "Area empty of matter" , "Nature is said to abhor this empty space" , "Space entirely devoid of matter" .)