When I run cli cache prune it does nothing and echos "Success: Cache pruned."
When I run cli cache clear it does remove cache files and echos "Success: Cache cleared."

Adding --debug did not add anything interesting to the output, as far as I could tell.

My environment is a CentOS from root within a perl script, calling with backticks:
sudo -u foo $php /usr/local/bin/wp cli cache prune --path=/home/foo/public_html
where
$php = '/usr/local/bin/php -c ./php-wpcli.ini';

The cache is, for example:
ls -1 /home/foo/.wp-cli/cache/plugin

akismet-4.1.6.zip
autoptimize-2.7.3.zip
classic-editor-1.6.zip
disable-comments-1.11.0.zip
jetpack-8.6.1.zip
jetpack-8.7.1.zip
jetpack-8.9.1.zip
loginizer-1.4.4.zip
loginizer-1.4.8.zip
loginizer-1.6.0.zip
master-slider-3.6.2.zip
page-links-to-3.3.4.zip
wordpress-seo-14.3.zip
wordpress-seo-14.4.1.zip
wordpress-seo-14.5.zip
wordpress-seo-15.0.zip

The file timemods seem to be the date the script ran.