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Syncing OmniFocus with iTunes and WebDAV both is technically redundant. (But that's kind of what backups are all about, isn't it?)

It probably comes down to a personal choice. Is it worth waiting a little longer* every time you sync in order to have your data backed up in two different places?

iTunes only seems to keep one backup at a time (so if it dies mid-back-up, you have none). It also doesn't let you selectively restore some stuff without restoring everything. And as far as I know, those backups aren't human-readable. It might be more worth your while to create a backup of the data on your WebDAV server occasionally instead. Copy those files to wherever you keep your computer backups or something.

*I don't have firm data on how much longer it is, so I recommend you test it for yourself once you've been using OmniFocus for a while and have a bunch of data.