It is perfectly acceptable to say "How much deposit". The reason why is because when you're referring to "deposits", you're referring to several payments or instalments. So while deposit can be countable, it is also very much an amount as well.
This allows both sentences to be equally valid:
"How many deposits do you have to make?"
"How much was that deposit?"
On a subtler note, while it's not correct, it may be more natural to say something like: "How much do you pay on your mortgage?"