One thing Apple won't remove are the volume up and volume down buttons. The original iPod touch was missing these and Apple said, "just use the touchscreen interface to change the volume."
That didn't change the fact that it was clumsier to change the volume with the touchscreen interface so they introduced physical volume control buttons on the second generation iPhone.
Let's say I'm walking around with headphones listening to music and my phone is in my coat pocket because it's cold out. I have to pull out the phone to change the volume? No, that's stupid and that's what many others said about the first generation iPod touch including me. I owned one.
Same thing with the mute switch. In many situations a physical switch is more convenient and quick to operate than an onscreen setting. Sliding a switch is far easier than pressing the home button, unlocking a device and finding some online "swipe to mute" switch, at least for a phone.
For cars, what is easier: navigating a bunch of windows on a touchscreen panel until you reach the environmental controls section or turning a big physical dial to warmer or cooler? (Or to turn the fan to High.)
Think about all of this, put on a pair of gloves then think about it some more.
I think an accessory port will be around for years. Eliminating all ports would make it more difficult to connect accessories, especially ones that require power to operate but do not have their own built-in power source (e.g., a blood glucose monitor). While data can be transmitted wirelessly, power is not so easy.
And as to data, using a wired connection is still more secure, both in terms of data integrity as well as privacy/security. Sure, Apple could remove all ports, but when you go to pay some vendor with your credit card, all of a sudden you are entrusting your card info to the credit card scanner manufacturer and their ability to secure the data transmission process. It's one thing to trust Apple and Verifone to handle Apple Pay transactions, it's something else to trust some tiny accessory manufacturer with your financial data.
Note that wireless transmission of data or other signals can have a strong effect on battery life. That's another consideration that Apple would need to weigh in before switching to an entirely wireless device communication philosophy. There's less overhead AND COST with a wired connection.
Walk into your living room and turn on a light. Now try to imagine a standalone bulb with no wires and what it would take to wirelessly provide power to light that up. Now think of what you paid for that wired light fixture.