I'm not sue https://developer.cisco.com/meraki/api-v1/get-organization-devices/ gives IPv6 details.
You don't say what type of Meraki device, but sounds like it may be MX.
These API calls get/update MX WAN interface settings, including IPv6...
https://developer.cisco.com/meraki/api-v1/get-device-appliance-uplinks-settings/
https://developer.cisco.com/meraki/api-v1/update-device-appliance-uplinks-settings/
Can't help with Catalyst Center itself, but back when it was called DNA it did not support many Meraki features, it might be you cannot do everything you want from CC.