Kevin, I'd like to propose an additional feature that I believe will complement large UR database management whichever of the above approaches is selected.
My suggestion is to provide the ability to export a part of the tree, be it a specific branch or a filtered view, as a separate UR database. In addition, there should be the possibility to "merge" another UR database into the one currently open, as a branch of the current tree. Personal Brain provides a similar functionality.
This way, a branch or category that grows out of proportion for practical navigation, can become a database of its own. Inversely, one can join several independent databases into a larger one if required.
I believe this will greatly enhance the program's versatility and potential for handling large databases.
Last but not least, you may want to take a look at how Sycon's IDEA!, which is also a one-document program, provides the ability to work with multiple databases:
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