Does my CASA B1.1 licence (without exclusions) allow me to perform an aircraft navigation system update?

Probably yes, depending on the complexity of the system. You are permitted to update software in an avionic system, provided that the following three conditions are met. (Reference: Part 66 MOS, Page 6)

1. The system has a discrete test function to confirm success of the updating 
2. The serviceability of any other system affected by the system is also confirmed
3. Only simple tests (i.e. “Push a test button with a Yes/No result”) are required to verify serviceability