The only advantage to upgrading is to do something like the following:
Rush research trade, build basic freighters, establish as many routes as possible.
Research sensors (and possibly military stuff but probably not worth it), design an upgraded freighter with LOTS of sensors so you get your freighters wizzing back and forth acting like a sensor net.
Build a STANDARD freighter, launch it but don't send it anywhere. Upgrade this freighter to the new design but tick the upgrade all of this design box. Pay the changes and wait. After a few turns all of the freighters in all your routes will resume their missions with their shiny new sensors and show you everything you have been missing out on. You can now also send your new freighter to establish another route, or "upgrade" it to a transport/constructer etc.