It is said that the letter ‘ñ’ was born in the Middle Ages. Monks living in monasteries were often given the task of making copies of large texts completely by hand; the printing press still had not been invented. To save time the monks used to economize the texts by creating their own symbols to represent such things as double letters. In the 12th century they used a kind of tilde above the letter ‘n’ to simplify the writing of such letters as ‘nn’, ‘gn’, ‘ny’ and ‘nh’.
Some Latin consonant groups ‘gn’, ‘nn’ and ‘ni’ evolved into a nasal sound. Each romance language represents this sound differently: it became ‘gn’ in Italian and French, ‘ny’ in Catalan and ‘nh’ in Portuguese. Medieval Castilian (Spanish) represented the sound with the double ‘nn’, which was usually abbreviated with a single ‘n’ with a tilde on the top; this became the standard form that exists today and it is called ‘enye’ (ñ). This new handwritten form was also utilized on other letters such as ‘aa’ which was replaced by ‘ã’, thought this didn’t survive into modern Spanish.
This linguistic evolution can be observed through some Latin words such as ‘annus’ which became ‘año’ in Spanish.
It wasn’t because it was written differently (it wasn’t, all literate people wrote in latin), it was because the Roman provinces had their own accents and in the “dark ages”, meaning the loss of central control over the far away provinces like Hispania and Gallia and Britannia, there was no longer a Rome. Languages change over time, and I bet anyone who has tried to understand even old Norse (basically 1000 years ago) based on modern norse, or old English based on modern English, or old Spanish, etc. It’s not going to happen.
The letter ñ is simply pronounced as a nasal n, close to the ng in angry, but nasally. Jalapeño should be familiar enough. I don’t get angry, I get stabby.