The tool will only check landing page URLs of elements that are enabled, and which have gotten some impressions in the last 30 days. This means it will check only keywords, ads, and sitelinks with impressions that are currently enabled and located in active ad groups and campaigns.
Optionally you can use the advanced setting Include zero impression entities to check the URLs associated with enabled entities that have not received a single impression in the past 30 days.
Regarding the number of broken URLs we show in the email, these are based on any URL that is broken (404). We were not able to check it or if it gave some response that the code isn't familiar with or the landing page contains the text provided. The system finds a total of such URLs for each scope and projects it.