When they designed and tested the iPad they intended there to be magnets to hold the case shut. So they made sure the magnets would not do damage to any of the components. It has to do with where you place sensitive components in the device, strengthen the area where the magnet would slam into every time you close the case and add components that would deflect the magnetic field lines away from sensitive components. They would also test how strong the magnets could be before potentially doing damage to the device. All of these design criteria is published to the manufacturers of the iPad cases so they can design their cases safely. Most notably the iPad does not use any magnetic storage which might get damaged by permanent magnets. There are still components that can be sensitive to the magnets such as the built in compass but as they know about the magnets during the design phase they make sure this will not case and damage.
As an example of how through they are when designing and testing their devices, when a hospital discovered that small quantities of helium would temporarily prevent iPads and other Apple devices from working they noticed a line in the user manual manual specifically warning the user against helium. Apple knew of this strange weakness already in the design phase and even included it in the user manual.
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