I don't know. I'm guessing partly because its older technology, and partly because it's rather expensive for what you get. In my mind, the real power of the Yun is to do as much as possible on the Linux side, and use the sketch as a barely intelligent I/O processor, using the Process class to talk between them. But this means that any advantage of using the simplified Arduino environment is minimized, as much of the work is in Python and Linux. Given that, there are cheaper and more powerful alternatives - for my current project, I threw together a quick prototype using the Yun because I could build the circuit on a proto-shield and prove the concept, but am now designing a PCB that will use a Raspberry Pi Zero W - smaller, faster, and MUCH cheaper.
I feel like a traitor...