I agree completely. Non-windows dlls don't belong in the output since those API are not provided by windows and will never be implemented in wine. I think it's best if they're removed from the database completely rather than having the script ignore them but I'm afraid when many apps are added it could become a maintenance nightmare.
Maybe it's enough if you maintain a list of unwanted dlls. If a new app is added which needs the same dll then you don't have to delete it again, it will already be ignored. That way the database might get bigger. Or the ignore could be already done on scanning.
bye Fabi