Andrew, I think "legacy" nails it. When AOLserver first arrived on the scene Tcl didn't have "array get" and "array set" operations and they were much, much less useful than they are today.
Jun, it would be very easy to write a generalized put/get proc to mimic the ns_set operations on a list of lists. After all an ns_set is just a list of lists! :)
I've been working on the partially refactored portals package (the one now in contrib). One bug I had to fix to get it close to working was to remove caching of ns_sets because an ns_set is a pointer to a local data structure ... can't cache that handle and see the local data structure in another thread that attempts to use the cached value rather than reconstruct it from the database. Oops ... one more nail in ns_set's coffin IMO.
