Ah you're right.
Actual issues get treated as in app purchases, so only the actual app itself gets stored on your computer, while the magazines get downloaded straight to your iPad...
So I don't think a direct backup option is available.
But I did find this on the Apple website:
Redownloading an In-App Purchase
If you lose your In-App Purchases because apps were accidentally deleted, or if you had to restore your device without a backup, you may be able to download some of your in app purchases again for free. Not all In-App Purchases are eligible for free download again.
Replenishable In-App Purchases and subscriptions cannot be downloaded again for free, and must be repurchased. Examples include but are not limited to: extra ammo, additional health, extra experience points, or other one-time services.
Non-replenishable In-App Purchases and auto-renewing subscriptions can be downloaded again for free. Examples include: bonus game levels, a map/city guide, a daily news subscription, or other recurring services.
To download an In-App Purchase again, you must download it from within the installed app using the same iTunes Store account name for the original In-App Purchase.
Transferring an In-App Purchase
Subscriptions and replenishable In-App Purchase cannot be transferred or synced to another iOS device. Non-replenishable In-App Purchases and auto-renewing subscriptions can be transferred to another iOS device authorized with your iTunes Store account. For example, if you transfer a game from an iPhone to an iPod touch, only the game levels will sync over, the extra ammo and experience points will not be transferred.
Since magazines are part of the auto-renewing subscriptions section, you should always be able to re-download them in the event you deleted them food whatever reason.
Still not optimal, but I guess that's what we have for now...
Unless you go for Zinio and buy from their site, in which case you might also be able to backup the files on your computer.
But I haven't tried it out enough to know exactly how that works.