I have just installed Cryptomator 1.4.0-beta2 (1194) on mac OS 10.13.6, which I use with FUSE 3.8.2.
Apparently there is not Spotlight indexing for FUSE volumes. This is acknowledged in the FUSE FAQ (https://github.com/osxfuse/osxfuse/wiki/FAQ#46-can-i-enable-spotlight-on-a-fuse-for-os-x-file-system) :
4.6. Can I enable Spotlight on a “FUSE for OS X” file system?
Yes, but by default, Spotlight processes running as root would not be able to access the volume, so you have to use certain mount-time options. See the answer to the previous question.
Question 4.5 is as follows:
4.5. I am trying to access a “FUSE for OS X” volume but I keep getting access/permission denied errors. I am doing this as root - what is going on? Is not everything allowed as root?
For several reasons, by default, “FUSE for OS X” allows access to a volume only to the user who mounted the volume. All other users, including the superuser are denied access. You can change this behavior if you need to. Refer to the allow_other and allow_root mount-time options.
It would be nice if, when mounting a volume using FUSE, Cryptomator mounted the vault with the appropriate options to allow Spotlight indexing.