Not interface list but bridge port, is to be expected when former interface and bridge are deleted from configuration. Are there any clues in the system log / system history?
Regarding the vulnerability found in 6.40.4:
If you're not sure that Winbox port is properly firewalled, upgrade to 6.40.8 (bugfix) asap. Make configuration export before upgrading (/export file=config.rsc). Reset all user account passwords after update. Check configuration thoroughly for malicious scripts, proxy settings and scheduler and remove those entries. Post configuration here (/export hide-sensitive) if not sure.
Check
https://blog.mikrotik.com/security/winb ... ility.html for more details on the vulnerability.