I may be imagining it, but I vaguely seem to recollect someone (maybe MB) in the 2.1 livestream mentioning a timer in relation to the barnacles . Perhaps this represents the ripening process & when ripe the MA pods drop?
Or I could just be imagining it- early morning, must have coffee!!!
I vaguely recall something like this as well, coupled with a remark that "scumming will not help". Time to re-watch that live stream, and to test another of my wild theories: Since the great reversion, I have watched twice how other commanders shot up the spikes of the Merope 5C barnacle. However, when I re-entered the game some time later (i.e. after the instance timed out), the site was pristine again.
It would not surprise me at all if the barnacle state is now an attribute of the game account, just like the discovery state of every star/planet/moon/station is. Time to do a tour of the other barnacle sites "confirmed destroyed" in Pleiades.