I created an encrypted, sparse disk image. I mounted it on a folder. Spotlight wasn’t finding files in that folder. In particular, they weren’t showing up in the “All my files” predefined search.

Solution:

sudo mdutil -i on /path/to/mountpoint

... Took me forever to find this. Sadly, it adds the volume to Spotlight, but not to the "All my files" predefined search.

BTW - Spotlight does the right thing with data from the encrypted disk -- it stores it on the encrypted disk. i.e. you get a .Spotlight-V100 created in your root folder for your boot volume, and you get a separate .Spotlight-V100 created in the root of your encrypted volume. The encrypted volume's metadata is kept solely in the encrypted .Spotlight-V100