It's correct thought you need a comma after attendance and the 'i' in 'if' shouldn't be capitalized. It is more natural to rearrange the words a little to: "If students are missing when taking attendance, please ask why they are not in class". Note that above it's implied you're asking the other students why the absent ones aren't there. That's the only possibility. If you wanted to ask the absent students later why they weren't there, you need to reword the sentence a little. Something like, "If students are missing when taking attendance, please ask them later why they were not in class.