Yes, Matomo (Piwik) works well with any IPv6 addresses. Here is further information:
Tracking API will track users with an IPv6 address.
Visitor Log and other detailed user reports will display IPv6 addresses.
IP Anonymisation privacy feature will anonymise IPv6 addresses.
Geolocating IPv6 does not work very well: most IPv6 will not be accurately geo located. A few Ipv6 addresses may be geo-located when using the PHP or Apache geo location driver. IPv6 geo location does not work with the Maxmind PECL driver (issue). Geo locating Ipv6 addresses may improve in the future as Maxmind (our Geo database provider) improves the accuracy of their IPv6 databases.
Logs containing IPv6 addresses can be imported in Matomo (Piwik) without any issue and they will be correctly parsed, anonymised (when applicable), stored and processed.
Here is an example of an Ipv6 address: