What I think would help any COW file system is delay snapshot (and clone) deletion longer, and delete in groups, which would result in larger contiguous regions being freed. When one container is deleted, a small amount of space is freed, and then may be used for writes, quickly filling up, and thus increasing localized fragmentation - or more problematically for spinning drives it's increasing seek times by causing recent writes to be scattered farther apart. To reduce read and write seeks, it's better to have larger free areas for COW to write to sequentially.

So it'd be nice if there were something like a "remove/hide" feature for containers, separate from delete or clean up, with a command that makes it easier to select many containers for deletion. At least on Btrfs this should be quite fast, and the background cleaner process that does the actual work of updating the ref count and freeing extents should have a priority such that it doesn't overly negatively impact other processes.

Some of this behavior may change on Btrfs as the free space tracking has been recently rewritten. Right now the default is the original space cache implementation, while the new free space b-tree implementation is a mount time option intended only for testing.