The Internet Mail provider will scan emails (for Thunderbird and other mail clients) that use regular POP/SMTP connections.
It will not scan emails that are received or sent using secure (SSL/TLS) connections (for scanning of those messages you need to use another program to manage the secure connection - STunnel is the best known).
It will not (by default) scan any emails received or sent using the the Thunderbird Webmail extensions (or other third party Webmail converters like YPops, FreePops, MrPostman, Hotmail Popper). If you need help with this just advise.