Hi,
NCrunch will only load projects that are either:
A. Loaded inside the IDE
.. or ..
B. Referenced by projects that are loaded inside the IDE
This means that if you unload whole dependency chains of projects, you can reduce the number of projects that NCrunch will load or consider at any one time. It also means that if you have one project at the top of your dependency tree loaded, then NCrunch will still load the entire tree, regardless of whether these projects are individually loaded inside the IDE.
NCrunch v2.11 introduced a feature that separates the NCrunch engine from the VS IDE, allowing it to run in a different process. This massively reduces the impact of the engine on IDE performance, especially when working with large solutions such as yours. If you haven't given the latest version a try, I highly recommend it.