i'm not really sure how long it takes. i'm guessing a few weeks with heavy riding? a month?
ask a wheelbuilder at a local shop, all i know is i had my wheels built back in november and they're still true. (miguel at affinity is that f'ing boy) i was thinking of maybe getting them trued in a few weeks.
if what you're describing is a 'clunk' i don't believe it's your spokes. did you try the play test on your headset assembly?
when they settle, it's just the wheel flexing and stretching the way a piece of wood would. swelling and shrinking and what not. some spokes will loosen/tighten. the wheel responds to weather and riding conditions to a lesser extent the same way as a musical instrument would.