I confess to being almost entirely ignorant of the fiscal/revenue area, but my first guess would be that either someone decided to have a little fun with a cute hole punch, or it was a simple way for an official to invalidate the stamp and keep it from usage. Dunno.
If these were used on a financial document, like a bank check or stock certificate, I would say they were punch cancelled. But a MNH example with a punched design is a puzzler. You might change your topic title to mention the star punch -- it would catch more eyes.
Since in theory, the tax was paid as soon as the stamp was purchased, it was only a question of what specific document it was to be used on. So cancelling it presented no problem; many US revenues were also pre-cancelled.