Like you said running NTSC software on PAL consoles "works" -- it runs too fast - this also manifests in audio, which is also programmed by the game and is based on the video clock. Some games do not refill the audio buffer in a deterministic way which results in a quiet pop/clicking.
Additionally RDP fill is affected causing slight timing errors that can accumulate, for example some Turok 2 cutscenes do not display at the correct time, Banjo Kazooie intro would probably be slightly mistimed, and so on. Running my MGC demo on PAL causes it to fall out of sync by several second by the time the demo finishes.
N64 does not generate strictly NTSC compliant timings... it's either too fast or too slow. So in buffered mode you will get a single duped or dropped frame every 6-10 seconds. You have to be watching very closely before you notice it.
When you are outputting 60hz, and the game produces 50hz, or vice versa, the UltraHDMI OSD will let you know - it shows a *!* in the corner of the screen when you have it pulled up.