The current behaviour is by-design. The reason is to prevent the recipient of the export from viewing any excluded child items via examination of the original email parent native.
Note: While these EML placeholder natives are considered to be slip-sheets, they are not included in the Slipsheet Report that can be generated from the production folder settings dialog (Figure 1).
Figure 1.

The current product behaviour is by-design.
This document family member (or some of its attachments if any) has not been included in this production.
This happens even when the email parent item is included in the production. This behaviour only occurs when at least one child item has been excluded from the production.
The following example shows the contents of "native" sub-directory from the production export of an MSG file with two text file attachments. Only the second attachment (P10000003) was excluded from the production:
D:\Exports2\0.6.33.2118168066\1.5.33.9097462566606602286\clearwell_export_0000001\native\0000001>dir /b
P10000001_Not_Included_In_Production_Slipsheet.eml
P10000002.txt
P10000003_Not_Included_In_Production_Slipsheet.txt
Note: This example also shows the affect on the exported filenames when the export option "Append slip-sheet reason to exported filename" is selected.