I'd like to know what advantage you think this would confer? Other than the space yard output, anyway.
The ships would have to be constructed normally, so none of the usual advantage of a large ship would be possible. There's no logical reason to 'add' them after the docking unless a refit is possible.
Now, there's the one possible use that I can see for this. Instead of having a spaceyard ship sit in one place for a year or more, build the parts of a station as seperate ships and have them move to the location where you intend to assemble the base. Then 'dock' them together and do a refit to configure the final base. Quite a nifty idea, and could be a useful tech advantage under some 'advanced construction' tech field.
Other than that, I much prefer the 'docking bay' idea where one ship can have a special type of cargo hold able to contain another ship. If you could build starbases with lots of docking bays you could conceal entire fleets from view.