The Hab was designed to be on Mars, unlike the laptops, which are implied to be off the shelf (or close to it). As the book mentions, the Hab was constructed on Mars. So it's safe to assume that the computers that are built into the Hab were components of the Hab that the Ares 3 team installed into the Hab's structure. The computers would then not be off the shelf, they'd be designed to work on Mars, especially under crisis situations like being exposed to the Martian atmosphere.
Also, as part of the Hab, we know from their construction methodology that the Hab computer would have been just sitting there on the Martian surface for an extended period of time prior to being installed in the Hab. Ergo, it is resilient enough for the Martian atmosphere.