Since version 1.6.0 you can enable/disable subcomponent feature globally. Disabling subcomponent from plugin's settings doesn't remove Subcomponent feature from administrative screen of the project and it doesn't disables JQL. It doesn't add subcomponent picker next to JIRA's component field. Although you can still organize components into component hierarchy and use JQL to query them it is effectively disabled for users. They will not be able to select component from component hierarchy.
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