I have a few solutions with over 100 projects, so I know exactly how you feel. Solutions containing some managed projects are especially bad. Disabling Intellisense helps a lot. I've never seen such problems from Visual Assist (or other similar refactoring tools), and that fills in a lot of the missing functionality from losing Intellisense.
I've also encountered some projects that had code that would cause the Intellisense thread to endlessly loop and never finish parsing the code. Most of those times we were never able to pin down the exact bit of code that caused the problem. Certain heavy use of templates and nested macros were often high on the suspicion list.
The only good way to be sure that Intellisense is disabled is to create a directory with the same name as the ncb file. Go to your solution directory, delete the ncb, and create a directory named your_solution_name.ncb. Because it can't recreate the ncb file, you'll get an error box to click through every time you open the solution, but that's a small price to pay.
Simply deleting the ncb will mean that VS will just create it again. The methods that I've seen from inside the VS options will turn off some of the features but will not prevent it from trying to parse all your code.