A secure on-chip NOR boot loader that deciphers an executable is super simple to implement, bordering on trivial. The main problems are:
1. it's a lot easier to brick a device, resulting in more warranty returns
2. once the Windows or Linux kernel is booted *it* has no idea how to check signatures or decipher anything; if it needs to do this it will have to make calls to the on-chip firmware for these functions, which means lots of specialized kernel knowledge how to even make that firmware appear in the kernel address space. The latter especially since the firmware will be non-read execute-only and may not run with caching enabled (since the cache may not honor execute-only). In addition, the driver needs to be tied into the kernel's exec code path, which doesn't have a whole lot of hooks, which in practice means implementing your own signature-checking/deciphering file system. I think WinCE has a secure boot feature, but undoubtedly MS charges an arm and a leg for it, and on top of that imposes certain system design limitations that makes it impractical (may not work on ARM/MIPS for instance). For sector-level encryption you need twice the NAND flash since the risk of bricking means upgrades have to use partition flipping schemes. (Which adds cost and/or board real estate.)
The basic, simple boot loader turns into a gnarly, messy, second-guessing problem that undoubtedly will have its share of bugs. (Which may cause the device to brick or allow circumvention.)