To stop links building the popular page edit nph-build.cgi and comment out the process for building it.
Under sub build_all
Put a hash in front of the call to build the popular links, e.g.:
# &build_cool_page();
That'll stop the page being built, and you'll also need to remove the HTML links to the 'Cool' page from your templates so you aren't still 'linking' to that page.