Hence, my question about POE on a mostly embedded platform (i.e. no NTP access): has experienced POE developers seen any degradation in system-keeping time when POE was active 24/24 over long periods of time ?

No.

As for your concerns, I don't know about Windows, but usually a O.S. Kernel has control about anything that happens on that machine, hence it shouldn't have any issues about keeping up with the time passing. AFAIK the clock is kept in sync with the CPU ticking. But I'm sure not all kernels out there do that.