Unless there's something to spot a dock restricted system before entering it, or an alternate way for big ships to achieve standard procedures like refuel and repair, I think it'd be a counterintuitive feature.
... why can´t space stations (of different kinds) also have different sizes for their docking entrances?...
I just realized that all player owned ships in ED has to be manufactured to actually fit the docking station entry door? Unless they are planning external docking? :S
For large mother ships maybe we can also dock by flying close to the station and send a small ship from the mothership to transfer the goods, if your in a hurry as big ships might take time to dock.
You could definitely have capital ships that can't dock and can only be repaired in the orbiting ship yards that built them. Then you'd get a 'hunt the Bismark' dynamic where they get chased back to the yard once enough opposition teams up and smells blood.