Configuration Manager is compatible with Jira Data Center. This page lists some recommendations to avoid performance problems during snapshot deployments.
It's highly recommended to leave the "Send ClearCacheEvent to clear Jira's internal caches after deployment" general settings option in CMJ unselected (as it is by default). This way CMJ will only refresh the caches of objects changed during deployment and not all the caches on the system. Jira Data Center replicates its memory cache across all other nodes using a specially configured Ehcache and RMI. User and group permissions are cached in each node's memory, among other data items. Which means, that if the Send ClearCacheEvent option is selected a temporary significant slowdown of the system can be experienced by the users. More details about Jira Data Center scaling can be found in this article.
Because of the cache replication mentioned above, deploying changes to the user management or permissions may cause a temporary slowdown for users if the system is under heavy load at that time. This shouldn't be as significant if the Send ClearCacheEvent option is unchecked.