The card is read once at power-up. The data is written during calibration, which happens at build time and once a year after that. The idea of removable storage for the cal data was that the calibration is for off-board optical components rather than those on the PCB itself. So a dead board can be swapped out in the field and the uSD card transferred to the new one.
Typically once per day, sometimes more. I don't know the details of the bootloader, we bought the OS off-the-shelf. From testing I know it only takes one O/C contact to hang the CPU during boot, and we have never had a problem here with fielded units.
Fairly benign, commercial-office-type environment, no extreme temperature, no severe shock&vibe. For a more demanding environment I'd be wary of using sockets at all. Buried in the spec for the embedded PC connectors is the gem "Max allowable disconnect time under shock : 1 us" I can't imagine some of the faster interfaces e.g. PCI, USB reacting well to this.