There's adapters that allow charging at the same time. I'm not sure why audio jacks are difficult to waterproof. Samsung managed it on a few models, so it's certainly possible.

Personally I haven't had a situation where I wanted an audio jack in years, I assume the extra internal space goes towards things like longer battery life or slimmer form factors; not nothing, but also probably not a big deal for most people.

It seems like laptops are doing the same thing: all external ports are USB, and any specific needs get handled with dongles.

USB-C ports are pretty flexible, you can split one into many, use them for video & audio, use them for power delivery & networking, and they can transfer more data per second than cat5. It seems like manufacturers are trying to make it the one port to rule them all.