I agree! The thought has also occurred to me that perhaps there should be a new overlay backend just for storing this kind of otherwise-unsupportable metadata, regardless of encryption. Maybe a similar concept to hasher with a local db but for other metadata, or else maybe a sequestered directory of sidecars on the remote, somewhat similar to chunker. Every option has some pros and cons.
I think it kind of depends on what your other remote is. If it already has fast checksums, there's no real advantage to wrapping it with hasher, so you may want to use it just for the crypt upstream. But if it has slow hashes (like local), or the wrong hash type, then there could be an advantage.
I am not yet very familiar with union, so maybe someone who knows it better can chime in about any union-specific quirks to watch out for, but I'm currently wrapping hasher in a combine remote and it works quite well. I found a few small surprises, but easily solvable. My setup is probably excessive, but one of my remotes is now 4-levels deep going from combine -> hasher -> crypt -> drive. It's rclone-Inception 