Not just the signal processing on the received data, but if you want to transmit something, you will probably be using one or more DDS channels to do so. Those may be in the FPGA, or external chips. Either way, if you are mixing the outputs of the DDS, being off by a single clock cycle can cause your transmitted data to be complete garbage.
With an FPGA and external DDS chips, this is difficult to do just because of mismatches in PCB trace lengths and/or small temperature fluctuations. With a microcontroller, it is nearly impossible to do even when using DMA because of memory bus contention.
Another source of cracking could be related to moisture in the SMD components. We do primarily small volume PCB runs where I work. In house, with parts stored here, pick-and-placed here, etc. We have had components crack as well, and I recall one of the suspicions being the source of the components. They were a supposedly reliable supplier, but components from them failed more often than those from another supplier so we stopped getting parts from them.
I am not sure if resistors are as prone to humidity effects, but if plastic parts are not humidity controlled before going into a reflow oven, they are prone to cracking. Even as a software guy, I have seen several brand new boards with cracked components on them over the last 15 years. Often the cracked components are difficult to find, since they are so small and do not fail completely (they are just off by a wide margin.)
It's not so much that you never have the headers... more that you don't always want to provide the headers to everyone (since they may contain things you don't want to share.)
If you have a Python code base and are looking to speed up some part of it, Cython is the way to go. Pybind11 and cppyy are more for cases where you have a bunch of C++ code that you want to provide a Python interface for.
If you have a C++ project, you want to have Python bindings, and you don't want to share your header files, pybind11 is the way to go.
If you want to / can share your header files, cppyy is a very convenient way of being able to call your C++ code from Python. I'm not sure if there is a way to use it without headers.
With an FPGA and external DDS chips, this is difficult to do just because of mismatches in PCB trace lengths and/or small temperature fluctuations. With a microcontroller, it is nearly impossible to do even when using DMA because of memory bus contention.