Smart mailbox for unread messages in Mail.app
Spotlight is responsible for searches, so I would add your home folder to the spotlight system preference privacy settings. 


Then say Ok to any prompts that mention search will break. 
Then remove your home folder and let the indexer re-index mail messages. 
Restart after 30 minutes if you don’t see an improvement 


There are more drastic and questionable options, but let’s start with safe and easy.