According to changes list posted by Steve... (emphasis mine)
1.
> Refuelling Orders
> ...
> Multiple spaceports or refuelling stations at the colony
will not increase the rate of refuelling.
2.
> Ordnance Transfer Orders
> ...
> Multiple spaceports or ordnance transfer stations at the colony
will not increase the rate of ordnance transfer.
3.
> Cargo Shuttle Bays
> ...
> Spaceports and Cargo Shuttle Stations can service any number of ships simultaneously but they
do not stack. In effect they count as a single Cargo Shuttle Bay for any ship at the population.
However, there is also a line
> They retain their existing bonuses to loading and unloading cargo.
Do note that this line come before "Cargo Shuttle Bays" rule post, so this may have changed...
So while it appears to me that nothing stacks, I am not too sure if multiple spaceports still make cargo loading faster like in VB