I may apply for some permits this year, however I'm not sure whether or not I want to camp overnight. If I get overnight permits can I just do a dayhike on either of the two days?
Well... the Wilderness Permit Office people frown on that. They want to make all the overnight permits available to campers. But it always happens where someone intends to backpack and stay the night, but end up exiting the same day.
If you started a dayhike the second day of your overnight plans, you could technically be cited, and you might well be, if you told the ranger in the field that you had started up that day.
What I would do is enter the lottery for the overnight, and accept and pay for that (if you actually win a slot). Then if your plans change: Check online a few days before the permit date, and if you see an open slot (due to cancellations), call the Wilderness Permit Office (not Rec.gov), and they will switch your permit. If that doesn't work, walk in to the Visitor Center and try to swap the overnight for a dayhike there. That should work pretty much all the time.