We use InDesign with Suitcase XI here (on Panther and Tiger), and have found fonts to be OK once sorted out. The main thing here is to get your head around the ways OSX sees and places fonts, and organise them as you need them. Also check and mend your fonts with FontDoctor, which comes with Suitcase (or it did with v. XI)
Here is a link to a post on the apple site that helps you understand what fonts are need by OSX, and where they should be. You can strip out others.
Please note that InDesign installs loads of fonts in HD>Library>Application Support>Adobe>Fonts. Only the fonts in the 'Reqrd' subfolder in the above location is needed, the rest can go.
Once you flush out all uneeded fonts, you can forget Font Book - it becomes irrelevant. You don't need ANY fonts in your user/Library/Fonts folder, BTW.