SYMPTOM
In Strategy Developer 9.4.1 and 10.x, set custom number formatting as the following to display zero subtotal values in report as blank:
0.0%;-0.0%;

On Web, zero subtotal values in report can be displayed as blank successfully, as shown below:

However, it is not retained when the report is exported to PDF and Excel file, as shown below:

CAUSE
When a report is exported to Excel and PDF file, zero subtotal values are in text format, not numeric values.
Custom number formatting is separated in three parts by two semicolons; only positive numbers, negative numbers and zero values are specified in the order. For the case of zero in text, it is not considered in the number formatting.
ACTION
Append one more semicolon in the custom number formatting to specify displaying text as blank as follows:
0.0%;-0.0%; ;