At the moment the only encryption that Atlassian supplies any support for is SSL/HTTPS. JIRA is not tested on encrypted databases or file systems.
That's not to say that data encryption isn't done by other JIRA users, either at the database level or the file system level. There are users that run such configurations. However, if any issues are encountered involving the file system or database encryption specifically, Atlassian would be unable to provide support for those encryption issues at this time.
There aren't any plugins that handle encryption and decryption of an entire JIRA database. There is a plugin that can encrypt and decrypt a single field in JIRA (It's called Encrypt Field)
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