There are a couple ways to deal with importing the various yui resources, yui+ext itself compiles down to a single file, and thats getting updated a heck of a lot more frequently than the actual yui components. I would probably recommend that the files were stored externally from any domino database in the html directory. This would make updating the files quite trivial. They are included with the Domino YUI database so that people can get up and running quickly.
If you were adamant about placing the files within the domino database I would recommend looking into using WebDAV.