Noticing I can get higher throughput with higher CPU on my Mikrotik PtP links, if I were to day turn up the CPU from 600 to 680, or even 800mhz, is there any dangerous risks? Why do they allow you to change it, if it will burn it up or anything???

It will not, but if you experience some sudden instability or reboots, set it back. We would not allow such setting, if it could burn your device.