When using the WHM interface, there is a global option to enable SPF & DKIM records to all domains on the server. This interface inside WHM is the following:
WHM: Home -> DNS Functions -> Enable DKIM/SPF Globally
However, using the cPanel API calls, you can enable or disable the DKIM record on individual domains. There is not a way to do this through the WHM interface.
For this procedure, you would need to be familiar with the cPanel API calls. The API calls can be used by command-line, also reachable by the WHM: Terminal Feature, to run certain cPanel functions.
To enable or disable a DKIM record for a domain, you will want to reference the following WHM API documentation:
Both of these API calls have a "command-line" component. Below are examples you can use.
To enable DKIM:
whmapi1 enable_dkim domain=cptest-2.com
To disable DKIM:
whmapi1 disable_dkim domain=cptest-2.com