Yes. Exactly right. The "should" expresses a more unlikely case than the simple past, and therefore the teacher's astonishment is even greater.
Note the three hypotheticals, in decreasing probability:
1. If ten students are absent (at least as likely as the students' presence)
2. If ten students should be absent (a possibility)
3. If ten students were to be absent. (a more hypothetical possibility)
In the construction with "that", "were to be" is not an option, but "that 10 students were absent today" is still less probable than "that 10 students were [=past of are] absent today".