This wouldn't be nearly as much of a problem if you could just scroll through a folder with mixed usable/unusable samples without getting popup errors constantly.
Pioneer, maybe consider just a red "no" sign, or strikethrough the sample name? And then you can throw big errors that pop up message boxes across the entire screen when someone tries to actually load an unsupported file, rather than just when they try and scroll past it.
Alternatively, a way to do sample conversion on the device itself would be great. The list of software licenses in the manual suggests that it's running some sort of embedded realtime linux, so surely setting up sox to convert to 44.1khz/16bit can't be that hard.