I'm guessing they lost their back issues due to neglect and sometimes tragedy. When people are first starting out they often don't think that in 30 years time they will want a physical copy of their joke periodical and warehouse space is always limited. When budgets get tight it is sometimes the storage bill that has to be cut.

Could also just be a joke - never know with the Onion ;)

They could have just lost them too, doesn't need to be nefarious.

Hard to tell if the onion is trying to be funny?

It was me. Just wait until they find out which of the 1920s issues I took.