If the pre-order bonuses come in a module file, you'll most likely be able to deactivate it in the start menu, like any mods you'll use. If not, good question.

On console, unless there's a way to deactivate module, I doubt it'd be possible.
AFAIK they're set up like DLCs, and some of the preview videos showed a "DLC" button or somesuch on the title screen. So I'm fairly certain you'll be able to disable the preorder bonus by disabling the addon.
That would be an interesting way of handling the pre-order item. By making them modules that are loaded like a mod or DLC, that would avoid the problem of players being able to get all the items by using console commands.
Still, it seems like a waste for Obsidian to make all these neat items, weapons, and armor, and then have large amounts of the player base unable to ever see or experience them.
And I believe the DLC button shown on the title screen is there in preparation for actual DLC in the future, much like the Windows LIVE button was there in FO3 even before it was really used for anything.