I love my little guy with long hair - it looks so good and shiny and pretty - but I know that sometimes, they just feel better with shorter hair. Luckily, his grows pretty fast. Also, sometimes, Mojo is mistaken for a "girl" with long hair - why? I don't know....is there anything that says a male Yorkie should have short hair??!!
I say, do what you think is best for you and him.