1. Do the shorter straws in the musical pipe make a higher sound than the longer ones?
[Does 'the shorter straws' mean all the shorter straws as in #2?]
2. They are the professors at/of our university.
['the professors' mean 'all the professors.']
In 1, since you refer to “straws,” I’d write “make higher sounds” — so there are all plural references here. And yes, by “straws,” you mean all the shorter straws.
Yes, 2 seems to refer to all the professors. If you want to designate certain groups, then you’d write “the engineering professors” (or whatever group you mean).
And I wouldn’t use “of” in this sentence. I’d use either “at” or “in.”