Question

Why is yes spelt with 3 letters but in Spanish it is spelt with 2

Answer 1

Simply put - Different languages, different spellings.
There are diff rent grammatical rules when it could to different languages. 
Hope this helps. 

Answer 2

Well, in all languages, words are spelt differently. Because of this, you won't have the same words in two different languages having the same letters. For example, milk in English is spelt with 4 letters, but in Spanish, it is five (leche). Although there may be some words that share the same number of letters, this doesn't happen always. So, in this case, it was just how the language was created.