Formula - these aren't saved in the database so no need need to encrypt-at-rest (which is what Shield Platform Encryption is)
Checkbox and Picklist - I had a discussion with the PM about this about a year ago and the answer was basically "we won't do this without also being able to resolve side effects - such as supporting searches, list view filters, report filters, picklist data changes, etc.
As for workaounds - you need to shadow copy (in Apex) these field values into custom text (encrypted) fields - then in Apex clear the values.
Checkbox -> Text with value "TRUE" or "FALSE" (or "T" or "F" - it is really your decision)
Picklist -> Text (straight copy)
You'll lose some OOTB benefits of these fields, especially in report/list view filters as users won't be prompted with the allowed value sets