Emacs can use GPG to encrypt files at rest pretty transparently. Just save a files with the extension `.org.gpg` and it should get encrypted automatically with Spacemacs (I personally use https://github.com/hlissner/doom-emacs/).
Note that adding an encrypted file to your agenda, .e.g.
`(setq org-agenda-files '("~/org/secret-diary.org.gpg"))` will let Emacs decrypt that file upon calling "org-agenda". Something similar should be possible for search if it doesn't work out of the box
I use this to encrypt files as well and I think Emacs handles this very well for individual files. It is however the notes management tool that doesn't support transparently search through multiple files.
I imagine what is needed is using gpg-agent to handle passwordless decryption of the files at rest.
Ah yes, I am using gpg-agent with my Yubikey - decryption would be tiresome without.
Well, org-agenda at least seems to support it through Emacs lower-level functions. Search is a bit more complicated, but should be well possible through hooks?
Note that adding an encrypted file to your agenda, .e.g. `(setq org-agenda-files '("~/org/secret-diary.org.gpg"))` will let Emacs decrypt that file upon calling "org-agenda". Something similar should be possible for search if it doesn't work out of the box