1-3) all the I/Os from Bela are connected to the Salt PCB, however only 4 analog I/O, the 2 audio I/O and 9 digital pins are in use on Salt itself. 4 analog I/O and 6 digital pins are broken out to a 20-pin connector that is used to connect to Salt+. This could be a place where you would add extra pots / switches, if you wanted. You could even jumper individual pins from the connector over to Pepper, and you'd be able to use half of its analog inputs, half of the analog outputs, the two buttons and 4 digital ins.
2) Can I use my own SuperCollider classes etc. as normal with the SC version used on Bella? Are there any restrictions I need to be aware of?
We are currently on Sc 3.10-beta1 I think, so it's a couple of versions behind, but I should be able to upgrade it to a more recent version "soon". I think you'd have to be aware of CPU limits, as the board is not as powerful as a modern laptop. @hypasus, @hallwrk and @jonathan have been using Sc extensively on Bela, so they may be able to give you their take on it .