[OrderlyTiamat]

It depends on how you do it. Org maintains a reference to what id's you use in links, so if you have an encrypted file with an id link, those links are active and you'll be taken to the right file when following the link (and asked to decrypt it etc.)

for example:

encryptedfile.org.gpg

* someheading

:PROPERTIES:

:ID: bf15277c-8505-4888-9497-a5533829217d

:END:

EOF

otherfile.org

[[id:bf15277c-8505-4888-9497-a5533829217d][this link will work]]

EOF

I'm not sure about agenda and file completion though.

[rodelrod]

Agenda opens every underlying file in the emacs session so I would assume it would work. I've never used encryption, though.