Does the 12 SCU of cargo space include the space for storing cubes of salvage, or is there a different hold specifically for that?

The 12 SCU cargo space is the cargo grid for both cubes and scavenged items which you wish to legitimately store. Of course, as in all ships, you can place items outside the cargo grids. However, this has downsides, such as your cargo not being secure and risking being damaged, as well as not being recognized or detected by the kiosk or sales interfaces as legitimate goods for sale.