fwiw I have never met a native English speaker who says "num-pee". Although -py = "pee" for most English words, this random made-up proper noun is yet again another weird English exception...
When you have a consonant and a Y, it's generally quite common for that Y to make an "ai" sound. Like bylaw, dynamo, kyle, lying, rye, xylophone. So I'd say that Python's pronunciation is unexceptional.
In the case of pyramid, it comes from French pyramide so it follows the pronunciation of French. It's worth noting that both pyramid and pygmy have alternate/misspellings that use "pi" which shows that their spelling as "py" is not very natural to native speakers.