When navigating to a Project Record, why is the Opportunities Subtab missing?
It is expected behavior that the Opportunity Subtab on a Project Record will disappear when Advanced Projects is Enabled.
This is controlled under Setup > Company > Enable Features > Company tab > Projects.
Enabling Advanced Projects will remove the Opportunity subtab (under Related Records tab) in Projects.
The ability for the standard Opportunity subtab to show with Advanced Projects is currently tracked under Enhancement 156827.