Zinc rot is not that common. Does it still occur? Yes is does. You happen to get an engine with rot - just bad luck. If you were to look at all the engines produced in the modern era (and mostly over seas), the majority are free from rot. When it does happen, it is frustrating. I've been collecting/operating Lionel trains since the 70s. In all that time, I had to replace one set of trucks on a freight car due to rot, and now I have a JLC GG-1 with rotted truck frames.
Will someone be making parts for these engines in future to get them running? Hard to say. Today's engines are more detailed and are unique. In the postwar years, a lot of parts were common across the line and production numbers were higher for each run. Part dealers can make out better casting replacement parts for postwar because there is a higher demand. Casting parts for today's more specific and low production run parts may not happen because there is little return on investment.
Technology is our best bet. With the introduction of 3D printers (metal and plastic) it may become affordable for part dealers to print replacement parts. This technology is still in its infancy. But I can see, as this technology develops, a user could scan in a good version of the part and then have the 3D printer print a replacement. I think this is our best bet. Then part dealers only have to invest in the tech which works for all parts.
In the meantime, save the engine for a future repair, sell it for parts, or be creative and make up something so it can still run. Maybe you can find a junker version and salvage the parts. I would not let one bad engine ruin the hobby. There are a lot of great engines/cars/accessories out there just waiting for you to enjoy them.
