But that space usually isn’t. No company would make a battery with a tiny little protrusion where the headphone jack once was. That’d cost a lot more, and make it a lot more fragile.
They’d be more likely to leave it empty, or fit something else in that space, like a third speaker.
Completely fine. There are multiple phones that have been out with waterproofing and headphone jacks.
It’s not that much more difficult to waterproof than the charge port.