The bad link report has functionality which allows you to exclude templates from being included in the report's results. It does not however exclude templates added in the workarea's template configuration settings.  

ekbadlinkrpt.excludes

In order to have templates not show up in the bad link report, remove the template from template configurations(workarea > settings > configuration > template configurations), add the file path to ekbadlinkrpt.excludes(located in '~/workarea/'), and rerun the report.