SAP allows you to define whether a database field can be NULL or not. However in order to make use of this you need to be able to write the database select yourself (to use the IS [NOT] NULL clause of the OpenSQL condition).
If you're calling a BAPI, it doesn't matter how the database table is defined, what matters is the interface of the BAPI. If the BAPI interface doesn't offer any indication whether a value is NULL or INITIAL (Zero), than I think you're out of luck. Your best bet would be to see if there's some way to enhance the BAPI to include an additional flag indicating whether the field is NULL or not.
