I've never heard of or seen a populated system without a nav beacon... even out in places like Coalsack or California nebula.
To my understanding, the purpose of a navigation beacon is to track ship traffic as well as monitor and provide information to local pilots on signals throughout the system, bodies and stations... perhaps also the state which it currently finds itself in. Maybe it also serves as a navigation aid for hyperspace jumps, but seeing how those can be performed in the furthest reaches of space without issue, only using the light of a star (or the absence thereof when it's a black hole)... not sure.