Software updates (including the device OS) are pretty commonly done via network connections these days, be they wifi or some other other network (LTE perhaps). Now, I'm not saying that your hackability argument has no truth to it, since over the air updates are often tightly controlled as to the source of the update, so installing a non-approved update might be trickier. In principle however, this depends far more on the specifics of the controls the device has put into place to stop unauthorized firmware installation than it does with the means of connectivity employed to make it happen. Keep the port if you have to, but I haven't connected my iPhone to a computer via USB for data transfer of any kind in something like a year now.
It could also readily be argued that re-flashing with non-standard firmware and low-level debugging aren't consumer features and thus don't represent a substantial use case to drive the inclusion of the port for the sake of the percentage of users that would actually use it. I could see a JTAG connection for repair and debug for instance, but why a full USB port?
MHL has seen relatively light adoption. There are other ways to handle A/V out than a physical connection though. AirPlay comes to mind. The bandwidth required to send compressed audio and video at with multiple digital audio channels, high definition resolutions and high frame rates is well within the capabilities of WiFi. I stream 1080p video to my Roku from my Plex server all the time over WiFi.
I guess what I'm trying to say here is that you can argue that a physical connection is somehow better than a wireless one on the grounds of it being faster, more secure, requiring less power, or whatever you like. The real question though is is the experience of plugging in a physical cable and getting those things more compelling to the consumer than the experience of getting "good enough" capabilities without the need for a cable? Once you pass the "good enough" barrier, the cable vs wireless argument is pretty much a done deal for most people.