Possibly. We should keep in mind that our knowledge of number theory is very limited. They are probably not really interested because it's all really obvious to them -- and has been for quite a while. It's quite amusing to think about how they might laugh at our encryption systems relying on simple discrete logarithm-problems etc. Not unlike we laugh at Julius Ceasar for relying on simple substitution.
Julius Caesar didn't have number theory nor computers so his cypher was actually pretty sound.
We have a pretty good idea about the limits of encryption. I doubt advanced aliens would have much to laugh about our current state of our encryption systems.
Considering that most people couldn't even read regular text back then it was definitely pretty sound, but that's not really my point.
We do? Got any references for that? Take RSA -- it's not even proven that breaking it is equivalent with integer factorization. Even if it was, there are no proof that integer factorization needs to be time consuming at all, there might very well exist an algorithm with polynomial complexity.
