Retreats in numbers, receiving permission (5)
I believe the answer is:
Here is my best explanation:
'retreats' is the definition.
(nook is a kind of retreat)
'numbers receiving permission' is the subsidiary indication.
'numbers' becomes 'nos' (I've seen this in other clues**).
'receiving' means one lot of letters goes inside another.
'permission' becomes 'ok' (what is said to give permission).
'nos' going around 'ok' is 'nooks'.
'in' is the link.
(Other definitions for nooks that I've seen before include "Cubbyholes", "Alcoves", "Secluded retreats", "Corners (that go with crannies)", "Crannies", "Recesses", "Niches and crannies" and "Sheltered corners".)