This are just old technical problems which are already solved, for example by Tutanota. Mails are not send in plaintext if they are encrypted, and mailbox can be encrypted too. Plaintext version of your data exist only in the memory of your computer while the session for your mail client is open.
What it comes to the search - it does not matter anymore. We have enough computational power these days and storage to hold emails on devices. User experience is about the same. Increasingly, it is just optimisation problem which can be done right. Just don’t use Electron for your email app.
But that is true that if you use skiff to send message for someone, who is not using skiff, the message is unencrypted because receiver has no means to decrypt it.
That is standrdisation issue. Apparantly PGP is not considered good enough.
But if we had standards, we have techology to provide E2EE emails.
Somehow the infrastructure should be transparent so that outsider can verify indeed at any time, that you don't collect logs from that traffic, or have no other means to inspect traffic if you want to.
There are currently no other means than just to use E2E encryption.
There is also another almost there, but that would mean that you should open-source your whole infrastructure, and use reproducible builds. Somehow there should be way to get access for outsiders, that you indeed use your infrastructure as you describe in your source code. But this is very complicated and also changeable at any time, unlike E2EE.