ISPConfig uses Linux system quotas for websites and not pure-ftpd quotas. Linux system quotas are handled by the filesystem automatically and are configured in /etc/fstab. They are used for ftp and ssh users, linux system quotas dont have to be updated manually with pure-quotacheck.
ISPConfig does not use a file called .ftpquota in its default install, so there is no need to update that from ispconfig side. If you use a different setup though, then you might have to use your own scripts.