Twitch uses a tool called Audible Magic that automatically scans your VODs for copyright music and mutes it. However, the tool is not 100% accurate. Copyright music can (and often does) sneak through, leaving you vulnerable to DMCAs.
When a VOD or clip is deleted from Twitch, it can take time for the content to be fully removed from the publicly available site. Twitch has stated in an official thread on Twitter that they cannot verify if third-party tools have fully removed content from their site and that content deleted using their mass deletion tool should not be subject to DMCA strikes.
However, users have found ways to access deleted VODs and some third-party sites are archiving content from top streamers on Twitch, both content deleted by the streamer and content from banned streamers. Twitch has not officially addressed concerns about publicly discoverable archives that may contain content that was deleted from the Twitch site.