However, when I open a recent file in InDesign CS5, half of the OpenType fonts are not found. What gives?
When upgrading the OS from Tiger or Leopard to Snow Leopard, Font Book's database sometimes gets damaged. When that happens, one common symptom is that fonts that are supposedly active don't show up in applications. The only fix is to clear it.
Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding the Shift key until OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally.
This will clear Font Book's database and the cache files of the user account you logged into in Safe Mode. Any font sets you have created will be gone. Also, all fonts in the three main Fonts folders (System, Library, your user account) will now be active, regardless of their state beforehand.