IPFS needs transparent encryption yesterday. I tried to start a discussion and even made a rough design but they don't seem interested.
They have added some basic protection where a node won't serve content to another node without knowing the CID but this isn't the same level of security as E2EE.
I think the encryption key should be transmitted with the CID but separable. So that you can pin data with just the raw CID but share data easily with CID+key.