Following best practices requires replacing empty values.
Applying this with a conditional fixed transformation per field is a tedious manual task, especially on tables with many fields. In a normal ETL you would do this with an ISNULL([Fields], 'n/a') function or by creating default constraints on the table fields in the data warehouse.
I'd like to suggest having a bulk transformation setting on the table level, perhaps only to apply default values. It would open a dialog with all the fields of the table, their data types, a checkbox and a dropdown populated with values configured on the project level where a data type has been assigned a default value. By default, the selected value would the one assigned for that data type with an option to set a new fixed value (like in the Table insert dialog).