Replies could be generated automatically. Since I presume they are checking applications on computers/tablets they could make checks next to each question. The person reviewing the application could simply check "Not good enough" or "Deal-breaker" next to the answer. It wouldn't be a lot but at least you'd get some idea on what needs improvement, and it wouldn't take much effort on their part. Or am I over-simplifying this?
It's not a matter of manning up or having respect. Do the math on what it'd take to email 3,000 rejected applicants.