At game start, my usual freighter is one hold, 2 shuttle bays. I dont bump that up until I have enough engine power and shipyard space to drive a large cargo bay.
Honestly, I use my freighters as seed ships to get colonies started, and then move a lot of the lift over to civilians. I drop initial infrastructure, a mass driver and automines into a system, and let the civilians handle the rest. It takes longer at start, but once you have multiple shipping lines going, its MUCH faster and cheaper than managing it all yourself.
Late in the early game/beginning mid-game, I use my freighters as express services for stuff that has to get delivered immediately, or to grab minerals that I need somewhere else fast. Even when I move to the express, I still dont tend to use more than 2 shuttle bays. Between the ship commander logistic bonus, and the colony logistic bonus (if any) its generally moving fast enough for me.