"Hvordanskriverdudinbog?"

she sounds sad when shes saying this

I would have said "Hvordan går din bog?" more friendly ;--)

shouldnt how do you write IN your book count too?

shouldnt the last two letters in the sentence be ER

So what does the Danish sentence mean ?

Can this be understood as 'in which language are you writing your book?' as well? If not, what's the meaning?

With a pencil.

This is a really strange sentence in English. If we were inquiring about an author's methods, we would say "how do you go about writing your books?" or "how did you write your book?" and then follow it up with a more specific question. If we wanted to know whether a writer used a pencil or a typewriter or computer, we would say "what do you write with?"