ISPConfig uses courier as default on debian as it offers more features like mail traffic accounting. If you dont need mail traffic stats, you can use dovecot as well. On some distributions that do not have courier packages, we use dovecot as default as there is no alternative available.
In general courier is as good as dovecot. They only differ in a fech technical details like the inbox format. You should be able to set this in your mailclient.
If you want to switch to dovecot, you would have to modify all inbox folders manually as the storage path for the mails differs.