Tente isso. Cria um array como no seu exemplo e apenas imprime campos mesclados via END { ... }
.
$ awk -F\| '{ k=$1 FS $2 FS $3; h[k] = (k in h) ? h[k]=h[k] FS $4 : $0 } END { for(x in h){printf "%s%s\n",h[x],(length(h[x])>38) ? "" : "|NA"}}' file1.txt file2.txt|sort
Student1|Class 1A|27|20140804 08:16:54|20140805 08:16:54
Student2|Class 1B|15|20140804 10:10:10|20140805 10:10:10
Student3|Class 1C|17|20140804 15:02:14|NA
Student4|Class 1D|20|20140804 18:02:14|20140805 18:02:14
Student5|Class 2D|10|20140804 20:02:14|20140805 20:02:14
$