Portuguese seems to have held onto a lot of medieval spellings and pronounciations as I notice Spanish and Portuguese use to pronounce Juan/João similiarly at some point in the middle ages, is this accurate?
I'm not super familiar with that particular bit of language history, but AIUI nasal vowels/diphthongs are just weird. The way we both pronounce and spell them seems to have evolved a fair bit. Joam and Joaõ are both obsolete spellings of the name, so I can only imagine that the spelling was closer to Spanish before and we've diverged more than they have.