Nothing electrically that impacts waterproofing, but if the headphone jack straddles the front and back covers mechnical sealing will be harder. I think USB should actually be more difficult to waterproof, since there's more spaces for drops of water to stick vs a "hole", the pins are closer to make shorting easier, and there's higher voltages being passed over the pins when charging. The only thing I can think of is that surface tension of water would prevent droplets from forming in a tiny dense USB-C port and not so in a 3.5mm jack, but that's a bit of a stretch.
