Theme of a thousand holy books — doubt (5)
I believe the answer is:
motif
'theme' is the definition.
(motif is a kind of theme)
'a thousand holy books doubt' is the wordplay.
'a thousand' becomes 'm' ('M' can be a synonym of 'thousand').
'holy books' becomes 'ot' (Old Testament).
'doubt' becomes 'if' (as in 'it's a big if').
'm'+'ot'+'if'='MOTIF'
'of' is the link.
(Other definitions for motif that I've seen before include "decoration" , "Distinctive idea or theme" , "artistic figure" , "Theme in music or book" , "Recurring image in design" .)