There is a maximum limit on Wonder Cards to receive Pokémon at some events. Is it possible to delete used Wonder Cards and keep the Pokémon they came with?
Once you have received the Pokemon or item in question, then the Wonder Card is essentially useless and can be deleted. Deleting the Wonder Card does not remove the Pokemon or item from your possession.
So if you did the Victini event in Black/White and received the Liberty Pass, you can delete the Wonder Card; it won't delete the item. Incidentally, once you have the Liberty Pass, you can do the Victini side-quest any time you like (well, almost - I heard that at some points in the story, when Team Plasma are tied up elsewhere, you cannot go to Liberty Island).
As long as you have actually picked up the Pokémon or item from the event, you can safely discard the Wonder Card in order to attend additional events. They aren't tied together past that point (as most directly evidenced by the fact you can trade away the Pokémon, which further distances it from your cartridge's Wonder Cards).