Well, ok, I guess we can use that as a justification for anything then. For example, the “good reason not to” use E2E for ntfy could be “market analysis says the small and somewhat theoretical benefit isn’t worth the complexity.”
Yes, but you said all private communication should be E2E. Apparently you're defining communication in some way that excludes an awful lot of what I'd consider communication (e.g. HTTPS traffic).
My key point was "unless there is a good reason not to". And in many cases there is a good reason not to use E2E encryption, like the example you have given. But in the case of Ntfy, E2E encryption would be a perfect fit, and eliminate any need for self-hosting.
I'll be blunt - as someone who worked in the space extensively... if you really need e2e encryption, you want to be self hosting anyways.
By the time you're trusting a hosting provider to properly do e2e for you... you've basically already lost the game. At any point they can update what's running and remove any/all protections you think you have.
So again - what is your threat model here? Because it sounds like you want "super convenient" and also "super secure" and those aren't two options you just check off - they're really more like diametrically opposed sides of the same slider.