When you opt your songs in for monetization via YouTube Content ID your songs are delivered to YouTube’s database. The audio files are then scanned against all videos uploaded to YouTube and claims are placed on any videos that contain identical audio matches. Future video uploads will be scanned against the Content ID database and are then claimed accordingly if matches are found.
The claims placed by YouTube on videos are not copyright strikes and do not negatively affect the channel’s standing; they simply enable monetization so that the copyright owner is paid out a share of the revenue.
Check out YouTube’s Content ID page for more information.