Found this issue https://jira.mongodb.org/browse/PHP-219 but nobody even voted for it for almost 2 years.
Not sure about mongo native support, but from MySQL practices:
You would have to do some PHP cooking before putting IPv6 into DB:
Use
inet_pton() http://php.net/manual/en/function.inet-pton.php
and
inet_ntop() http://php.net/manual/en/function.inet-ntop.php
And then store IP address as binary data.
The PHP driver supports IPv6 fine, as long as you use a hostname in the connection string. The connection string parser currently doesn't understand IPv6 address notation yet, but that's tracked through https://jira.mongodb.org/browse/PHP-524