While this practice definitely is loosing coverage, you'd be astonished by the amounts of USB connectors that have been glued down on desktop machines in corporate office environments. And I'm talking large multinational corporations here.
But now on topic...
For commercial projects where the IP protection is a major factor, the Pi is good for early prototyping / proof of concept at best. Even if protection would not be an issue, deployments of the Pi on a larger scale is IMHO not the best solution - for a number of reasons I described in an earlier thread on this forum.
There is no system safe against reverse engineering / hacking / reproducing. Any system is exploitable. Every system however has a penetration score. With its open approach and external SD card, the Pi has a very low one. A custom designed military-approved hardware board with custom SoC, sandwiched components and multi layered PCB in combination with a custom bootloader, hardware encryption will have a higher score.
On top of that there is the deployment factor. The wider your market is, the more interesting it will become for people to break in and steal your technology.
If the hardware is your piece of resistance in the whole setup and protecting your technology is a major factor, I don't think the Pi is the product for you. If your hardware is a facilitator for selling services, perhaps protecting technology should be done on the server side rather than on the client side.
We use the Pi for selling such services. Our software on the Pi does have a raised level of protection, we're using a compiled C application, locked on MAC and/or CPU serial number. But at the end, without our server side, even the source code is virtually useless.