It's a good point, and you don't want to avoid encryption just because of keys, but it's not quite the same as a backup. Often we have daily backups, and we store off the backups in multiple places (disk and tape).

However with an encryption key we have to protect that in a different way, and storing it with the backup could be another issue. Add to that the need to periodically rotate keys, and you have another issue of knowing which keys go with which items.

It's the same problem, but an order of complexity higher. More moving parts.

In my mind, you need a secure storage solution for keys, one with rotating keys, but a way to track them. Maybe as simple as two piece of paper stored in two secure locations (safe deposit boxes, safes,et c) that you can get to if you need to.