Anything that couldn't be targeted by the original spell (due to shroud, protection abilities, targeting restrictions, or any other reason) is just ignored by Glimmervoid Basin's first ability.
Glimmervoid Basin
A face-up plane card that's turned face down becomes a new object with no relation to its previous existence. In particular, it loses all counters it may have had.
Other than choices involving modes or additional costs, the copies are created based on what they could target if the spell were cast anew. For example, if a player casts Naturalize ("Destroy target artifact or enchantment") targeting an artifact, Glimmervoid Basin's first ability will copy it for each artifact and enchantment it could target (and each copy will target a different one of those), not just for each artifact it could target.
Magic: The Gathering · ™ & © Wizards of the Coast · Illus. Lars Grant-West
Card data via Scryfall. Rarix is fan-made; not endorsed by the rights holders.
