After years using font management applications (Suitcase, FontExplorer) a couple of years ago suspicion of corrupt fonts led me to strip down to using just FontBook as a minimalist font management tool. It is very cumbersome though that even though in FontBook I deactivate all the fonts I'm not working with or wanting to explore, a huge list shows up in my Adobe applications. How can I control/sync my preferences for which fonts are active or not? I'm a graphic designer, so this is a real annoyance.
You cannot deactivate fonts when the are installed as system fonts. But you can install fonts for some software manufacturer like Adobe for them only in the Application Support in their subfolder is a font.
With InDesign you can also install fonts for InDesign only in InDesign's font folder.
With in InDesign you can also install fonts on a Document level only, if you place them in a folder named "Document fonts" which has to be in the same directory as the INDD file is.
But with the current CC versions you see in the font dialog a star at the left of the font's name. Click on this star, then it will become a Favorite, and then you can click above to filter your favorites only. This will hide all other fonts. This may work for you to reduce the list.