You’re right, and it’s probably important to game out what the purpose of such an ark is.

Are we trying to revive a set of animals that have gone extinct on earth, but there has been continuity in civilization from the time we placed the ark to when we need it? In that scenario we could have just taken the necessary effort to protect the ark from weather events. (Or build it sufficiently protected inside a mountain or whatever)

Or is the purpose to help an alien civilization (or a newly sprouted human civilization after some disaster) to recreate extinct life? In that case, I’d argue we don’t have the technology to ensure the ark is protected/intact over that time period whether on earth or the moon. It would be an extremely expensive undertaking we have no chance of ever seeing benefit from, and no way to know if another civilization would.