Agree with Tomalam, by making the hole in the SW assembly should not make the difference between your parts, the problem is that the hole will only appear on the assembly plan! Beware of forgetfulness!!
To exclude a feature from the list of welded parts:
Right-click the feature.
Select Exclude from the list of welded parts.
The next time you refresh the welded parts list, the function will be excluded. To include a feature that was previously excluded, right-click and selectAdd to Welded Parts List.