I basically agree with the posts from hippo, haukex and LanX

There is no need to put a reference to a course hash table in the student structure.
Put the course hash key instead.
A Perl hash lookup is very fast..

If the number of students or courses is "small", there won't be a performance problem.
"small" in this situation is like 100,000.
If one of the tables is more than that, then an SQL DB will yield better performance.