No it can't. The goal of popularity-contest not only collect what
packages are installed, but also determine what packages were recently
used. In order to do so, It checks what files are currently open and
scans last access time for files belonging to installed packages.

Probably, you may ask an option to disable collection of usage
statistics, but it probably makes popcon results less usable. Such
request should be forwarded to upstream developers in debain BTS, I
think.

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https://bugs.launchpad.net/bugs/493852

Title:
  popularity-contest will stat() every file installed file or ~80k files
  on my system which grinds things to a halt

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