Null values will be exported as just that - a null value. To get records from one table to be appended to the export of records from another table, within Filemaker, requires the use of an additional table. You'd need to setup fields in this 'export' table to match your source tables, then import from each of your source tables into the export table. Then, export from this table.
Here's a question - why is your data in separate tables if you want them to be exported together? And, what is your export file format?