What is the use case of a SD slot on motherboard?

Solution 1:

It's for booting a hypervisor or lightweight operating system like VMware ESXi.

See: What happens when the USB key or SD card I've installed VMware ESXi on fails?

Solution 2:

By installing an embedded hypervisor/OS on the SD card, you leave all the front-bay disks available for data storage. This is an useful logical and practical separation.

Some servers have two RAID1-ed SD slots: if a single SD fails, the system continue to run from the mirror, leaving you the time to replace the failed SD.

The most widely installed embedded hypervisor probably is ESXi, with a footprint less than 2 GB.