Nobody knows the true situation with the remote and obsolete parts. However, I worked in aerospace for many years, and many of our designs faced parts obsolescence. That didn't stop us from producing product, you just have to plan for it. It's very rare that you have to completely redesign a product for one or two parts that go out of production, normally it's a much smaller task to continue the product production.
I personally have used both the Lionel and MTH smart device applications, and I still prefer the remote. One thing that you can't do well, or at least most of us can't, is run one-handed with the phone or tablet. I also can't use tactile feedback on the remote, so I'm looking at the phone instead of looking at the train. When I'm running trains, I really don't want to stare at my phone all the time.