Please reach out to our support team to give you the ability to enable encryption on managed custom fields.
Please be aware that by enabling encryption on your custom field, you might prevent further upgrades, in case your package vendor adds non-shield compliant functionality against this custom field.
Documentation Link
Encrypt Custom Fields in Managed Packages
When you install a managed package in your Salesforce org with Shield
Platform Encryption, you can encrypt custom fields in the package. You
can encrypt any field that belongs to one of the encryptable custom
field types.
As an admin, this may increase the range of packages you
can leverage, because more packages will be encryption-ready out of
the box. (Not all of them, though! Check with the app vendor that a
package is compatible with encryption before you install it.)
Important Engage your app vendor to make sure they are prepared to
support encrypted custom fields in their package. Then contact
Salesforce support to enable this capability for your org.
If you’re an app vendor, talk to Salesforce support about getting set
up to support customers who encrypt custom fields used by your
package.