The relevant parts of HIPAA are the duty to not disclose PHI to unauthorized recipients and breach notification requirements if you do incorrectly disclose PHI (the HIPAA breach notification rule).
The magic of encryption is that HIPAA provides safe harbor if the data stolen/lost/intercepted was encrypted to certain standards. So if you lose an encrypted hard drive full of PHI, or someone breaks into your servers and steals encrypted data but not the decryption capability, then it's not considered a breach under HIPAA and you do not need to notify anyone.
Tons of PHI isn't stored encrypted at rest. Physical theft of the hard drive from the practice's back-end EHR database server hasn't generally been high priority on the HIPAA breach potential risk assessment list. But nearly all data in transit, on employee laptops, etc. will be encrypted, because that's where you want the safety net of the safe harbor provision.
