Physics Sandbox-Game

Hello there,
I recently played a Game called Scrap Mechanic. Its a Game where people build custom vehicles out of different blocks, thrusters, motors, etc.

Now I would like to make a Unity Clone of this game just for learning reasons and I want to ask for some best practices to do such a game.

The first problem is how do I attach different types of blocks(Different Size, Weight) to each other.
On Solution is to use some Joints to attach them but I think if I build a large vehicle with a massive amount of Joints the Physicsengine of Unity will hate me. So I have to create a DataStructure to combine them into one bigger object.
On possibility would be to use an Octree or an Array to combine them but there is none of them is as flexible as needed.
Maybe one of you have a betetr Idea for a Data Structure like this.

Kerbal Space Program also builds custom (space) vehicles out of different blocks and, as far as I know, they use standard Unity joints for putting all them together.