It sounds like you need to go to the Suitcase website and look for a help file, FAQ or forum to ask this question.
I've asked the question over at Extensis...
But the list is there in InDesign, even if Suitcase is not running at all. Where is that list coming from then?
I also discovered that the same thing is happening in Photoshop and Illustrator... the same list of fonts showing up even though none of those fonts are activated in Suitcase. They are not in any system font folder, or other unexpected folder, that I can find.
Ah! My business partner actually found the solution!
On the hard drive (not in the User) there is a folder called Library.
In that folder is a folder called Fonts. This seems to be a place that Adobe looks at for fonts.
I deleted the fonts from that folder (you could just put those fonts into another folder if you want to make sure you're not tossing an original) and those fonts are now gone from the font menu!
However, there are still some fonts there... so there must be another font folder somewhere... going searching now...
Well, if you have a Library, you must be using a Mac. There's an unfortunate number of places for you to look:
/Library/Application Support/<name of vendor>/Fonts
Those last two are unlikely locations. However, there's another group of folders where you should look. We don't know what version of ID you're using, but every install of ID has a folder called "Fonts" in the InDesign folder in the Applications folder, and the fonts in that folder are only available to that installation of ID. On top of that, I suspect that you already know that the fonts in your Document Fonts folder located next to your InDesign file will load up when you open that InDesign file.