If you have agents mapped to domains, a user with SuperDomain permission would still be able to see that data.
Agents can only be in SuperDomain or one custom domain - they cannot report data to both the SuperDomain and custom domain at the same time.
It's unclear where your agents are reporting at the moment, this is documentation on mapping the agents to domains
Define and Configure Introscope Domains - CA Application Performance Management - 10.1 - CA Technologies Documentation
APM 10.1 introduced a feature of dynamic domains, if this is turned on, agents can change mapping to domains without restarts.
The domain forms part of the full name of the agent, If the domain of the agent changes, the product sees this as a new agent, this breaks the continuity of historical data, this should be taken into consideration when making domain changes.
You can use agentclusters.xml to copy data from agents reporting in SuperDomain into one or more custom domains but this should be used to only report metrics that you need to report, not to copy the agent's whole set of metrics.
Configuring Virtual Agents - CA Application Performance Management - 9.6 - CA Technologies Documentation
If you are using things like Management Modules, if the Management Modules are in domains, they would not be able to access the data in SuperDomain, management modules also cannot make cross-domain links
If you want the metrics in the domains, it sounds like agent mapping to domains is the best option for you, taking into account the possible initial loss of historical data (although the old historical data can still be mounted as a separate agent)