DVD and DAT used 48 kHz as their base rate, while CDs used 44.1. This setting on the PS3 is for CD playback only. I think Sony made it a choice, and defaulted to 48 kHz because for digital transfer to a receiver, they all support 48 kHz, and while most support 44.1, the upsampled rates of 88.2 and 176.4 are less supported. Handing a receiver an unsupported sample rate can do anything from produce silence to a speaker/ear destroying screech (if the volume is turned up). So 48 kHz is safe.
The HDMI interface is able to tell the PS3 which audio rates/formats are supported by the connected device. But when using the optical connection the user must check the right boxes. One thing, DTS-CDs don't work when upsampled. Going to the output settings and unchecking 88.2 and 176.4 while using the setting I mentioned before, will make DTS-CDs work correctly, and not really have any hindrance on any other discs. Well, it will affect SACDs, but since most PS3s out there don't even support SACD playback it's safe. Though if you do play SACDs, you need to choose between them and DTS-CDs (or change the setting each time).
