Filter conditions for reporting should include records that have no value.
According to the Knowledge Base article, filter conditions such as the following will not include records that have no value for the filtered property:
is not equal to any of
doesn't contain any of
has never been equal to any of
has never contained any of
is not equal to
is none of
When filtering for deals in the Deals page, using these conditions would show deals that have empty values in the filtered property.
This needs to be consistent with the reporting tool!
The current workaround for this would be to use workflow to populate the empty fields with a custom "blank" value so that they can be included in reporting. This can get really tedious if there are multiple properties to be reported on.