As you can see removing: exec("rm -d -R /usr/local/pkg/vnstat2"); The uninstall will not cleanup the folders. Below is after uninstall with that line commented out.

[2.1-RELEASE][root@.]/root(1): find / -name \*vnstat\*
/usr/local/pkg/vnstat2
/usr/local/pkg/vnstat2/vnstat_php_frontend
/var/db/pbi/.hashqueue/vnstat-1.11_1-i386
/tmp/lighttpdcompress/vnstat2
/tmp/vnstat2.info
/cf/conf/vnstat
[2.1-RELEASE][root@.]/root(2):