I think shuttles (drones) are made as a separate 'submarine', which you then attach using the sub editor. I've never done it myself so not familiar with the exact process, but have a look at one of the vanilla subs that comes with a shuttle / drone to see how they did it. I think you specify the drone rather than add the whole thing, then there's a holding space for it. Probably talking out of my behind at this point!

Sure it can be done, but the problem is getting the workshop shuttle in the first place. It is a separate Submarine file and its file is not always included with the main submarine.

If it is or you somehow get your hands on it, sure, nothing's stopping you. It's not like a workshop sub is alien.

You just have to make sure that all the wifi components on the shuttle are on the same and frequency with the controls inside the main submarine.
Then you replace the existing shuttle with the new one, making any necessary adjustments (like docking hatch placement or making sure there's enough space for the new shuttle) and it should work.

You have to add them in the editor. Look at the top of the screen for a sub selection tab, and select your sub of choice. The sub will appear as a green outline of it's shape. When you place it somewhere (I prefer near the docking port), you can link it to the main sub port (If it is the same type, you can't attach vertical docking ports to horizontal ones, or at least i think so), by holding space and clicking on the port while having your shuttle selected.
So basically:

1. Select sub of choice
2. Place it.
3. Link it to the sub port.

Hope this helps!