Based on comments from Omni in a
previous thread, it sounds like this is strictly a manual procedure for OmniFocus 1.0. However, there may be plans to automate transaction coalescence in the future, perhaps with a tie-in to iPhone syncing.
I simply make it a habit to rebuild my database every couple days or after I've added a lot of stuff or made big changes. I then immediately follow that with a manually-triggered database backup, which can be found under the same menu item.