It is better to just follow the dad religion... unless your wife is a muslim... write something, don't left empty... don't play around with birth certificate...
You son can pick up the religion he likes when he is 18 and update his IC.

All known that at birth, the child had no knowledge and cannot choose about the religion. As a matter of fact, a child cannot choose his etnitcity, gender, name... etc.
So as parents, you fill in your part of information.
The pre-set mind about your child religion does not come from what is printed on that piece of birth certificate but instead his surrounding and up-bringing from parents, grand parents, relative and friends and his own discoveries.

As a matter of fact, ones religion in birth certificate does not represent his religion later on. Some of the chinese converted to Muslim still have their birth certificate set as buddhism despite they are now Abdullahs... On norm, one cannot change his/her birth certificate.

So, in short just put in parent religion.

But anyway... you are always welcome to check it out at JPN as suggested and feed us commoner more related information