It's not about whether users aren't smart enough for tags. It's whether tags work the way users want them to.
Tags are for organization. People like to organize things in terms of visual hierarchies and landmarks. Raw tagging systems aren't popular, because most people don't memorize precise strings. [1] They remember roughly what directories look like and 'know where things are' based on whether they believe they can confidently determine "it" from "not it" while they navigate a structure.
e.g. Was the tag "RaptorX" or "2012 Predator" or "FooBird"? The user doesn't know. But they do know that when they navigate their project folders, they'll be able to pick out whichever project was fuzzily translated to "something like a bird of prey" in their mind. And they'll be able to do this as they navigate into a tree, as fast as if they had remembered exact strings. [2]
So when people are looking for something quickly, they're going to like the visual hierarchy. And when they're first saving a file [3], or when they're looking to open something when they 'know' where it is, they respond very positively to a visual hierarchy.
It's not about 'hiding' the fact that those 'folders' are tags. Or hiding the fact that files can live in multiple places (with multiple versions no less). We're still talking about new software that people would have to be trained on and told about its particular attributes.
So the fact that, yes, you need a dialogue to capture explicit intentions when doing move/copy operations in a pseudo-folder tag system is not a problem.
[1] Also why command line OSs and command line navigation are unpopular. People really like visual organization.
[2] In my experience, this is what people are really saying when they insist they'd rather navigate than search, even when they 'know' where something is. It's because they "know" where something is, in terms of landmarks in the visual tree. They know in a fuzzy way. And fuzzy searching is either frustrating, or requires nailing down enough tangential data (user/date/file type) that searching isn't any faster than navigating.
[3] Almost no-one wants to think about proper taxonomy or organization or an exhaustive document profile when they're drafting a new document. They just want to stash things somewhere where they can find them tomorrow and/or reasonably direct a third party to them. Proper organization is almost always a discrete mental process that happens after a document is 'done'.