Well, like the OP suggested, if there were a few cancellations prior to the 24 hour mark, then there is a very good possibility that the upgrade would clear just before the 24 hour mark. There has been a lot of anecdotal evidence, as well as commentary from CO Insider to suggest that CO will often release all but one or two seats for upgrade/award at the 24 mark. So a flight that was J1 at T-28 could easily go J3 at T-25, and if the upgrade waitlist were still in effect, there's a good chance the upgrade could clear.
CO would have no way of knowing for sure that the 15 other J pax were 100% locked and loaded, other than to look at historical patterns. So it still doesn't make sense why they would cancel the waitlist.
I agree that in many instances it wouldn't have made a difference, but given the possibility that it could have, CO probably should have kept the list.