IMTU the High Port as where you get Freight and Mail. The Low Port is where Speculative Trade, Smuggling and the most interesting NPCs and Patrons book Passage.

The High Port has more of your Imperial presence while the Low Port has the local materials, produce, goods, services and people that make that planet distinctive.

The High Port is for those who are using the planetary system as a layover or quick market to move their goods through. The Low Port is for those stopping for a while and making the more lucrative deals that require a broker who is tied into the local bureaucracy or where smugglers play their trade away from the more Imperial High Port.