The probes cost enough to exceed individual purchasing limits at hardware companies, which means you need to go through the requisition process. That takes long enough that you have to plan ahead and you don't order more as your needs increase. Then everyone's fighting for the limited probes right before a ship date and they get jealously guarded like priceless jewels.
JTAG also isn't usually exposed through enclosures, so using the probe on a field unit might require destructive entry depending on the application.
Well the problem there is companies who are too stupid to invest in cheap tooling with massive ROI for their developers. A pretty constant problem in software development.
And I am not knocking JTAG over USB. It is certainly convenient and beneficial since you can enable it in production or deployed units. I was commenting on how the GP (and even article) was making it out to be missing capability. They just do not have the cheap tools that are the intended way to access that capability.
edit: The article even mentions how the "Qualcomm Landing Team at Linaro", which seems to be the team that works with pre-production hardware to get them working on launch day, has a development process where "debuggers have never been a staple of our work for all the typical reasons you'd expect (cost and complexity being the main ones)". That is literally the team that should have pre-production units in the lab which will have debug connectors and where JTAG probes should be par for the course, yet they are apparently hardly using them partly because of "cost".
The landing team's job is to "land" patches into upstream. They take Qualcomm code and spin straw into gold until it's eventually good enough to contribute to projects like the Linux kernel.
Having read a lot of Qualcomm code myself, I don't envy their job.
There's something wrong if you're using Jtag on a field unit. In my experience, once a chip is up and running we implement higher level communication and debug methods.
To give an automotive example, a field unit may fail and be RMA'd to the tier 1 to improve their production line. They don't have access/documentation for the production software, and it wasn't developed to interact with their diagnostic tooling. They'll need to reliably reflash their own test software onto a board with potential hardware failures. JTAG is sometimes what they request to do that.
JTAG also isn't usually exposed through enclosures, so using the probe on a field unit might require destructive entry depending on the application.