I think I know what's going on here, Boodster - when a file is deleted, the information isn't actually removed. What happens is that the space on disk that file occupies is added to a list of spots that new files can be written to. The amount of space the file takes up isn't that big an influence on how long it takes.
What matters a lot more is the number
of files - and in the case of an OmniFocus backup, what looks to you like a single file is actually a container for a collection of files. (You can see this by control-clicking an OmniFocus backup, then choosing "Show Package Contents" from the menu that appears.)
That said, an hour to delete 50 backups is a lot longer than I'd expect. If you contact our support ninjas
, we'd be happy to investigate this with you.