As long as you're convinced that your ionized air gun is not a static generator, it should work fine in dedusting your boards.
As you say, covering your board racks while the boards are being stored is probably a better solution. If you google 'esd cart cover' you find some contacts for cart covers.
(http://www.smtnet.com/Forums/Index.cfm?CFApp=1&Message_ID=65960)