When I was testing how a project would perform with large numbers of site nodes, I came across a similar problem. The way I went about tracing the issue was to stick a bunch of statements like the following:
ns_log Notice "[clock clicks -milliseconds] entered blah.tcl"
...into the tops of each main Tcl script and template script that got called in turn, so that I could get a rough idea of which Tcl file was taking the time from looking at the error log. I also wrote a little 10-line Perl script that could take these log statements and calculate the deltas - though that's more for convenience than anything (can send you the script if you want, let me know). Once I'd found which scripts were taking the time, I added more logging statements like that to track which Tcl calls were to blame until I isolated the problem. In my case (on OpenACS 5.0-based system), I tracked it down to site_node::get_url_from_object_id which used to scan through the entire site nodes nsv to get its result. A glance at current code makes me think this issue is fixed in 5.1 with an nsv set from object_id to url.
