I'm reading it as your plan is to hierarchise things a lot more than they are in the general "flat namespace" wiki idea - is this what TWiki "topics" are all about? I do prefer having a flat namespace and letting structure evolve as the wiki is used, but I don't object to building in hierarchy support to CGI::Wiki if people want it. It is not going to be a high priority for me unless someone makes it worth my while though - giving me good reasons to do it or offering to do some of the work.
Speculation: one could emulate a hierarchical namespace by differentiating between an item's name and title. The "name" would be some uniquely identifying #, while the "title" would be what humans see. Then hierarchical relationships could be represented in the metadata... (Perhaps this would require explicit CGI::Wiki support to keep the front end script from becoming a mess? I don't know.)
See: http://the.earth.li/~kake/cgi-bin/wiki-toolkit/wiki.cgi?node=Name%20Vs.%20Ti...
Personally I would like to see Wiki::Toolkit explicitly differentiate between name and title (really just as a special metadata) so that it will be easier to do things like this: http://www.usemod.com/cgi-bin/mb.pl?FacetWiki
Justin