Particle は is very tricky. In this case, you could add は after ジョンさん. It is grammatically perfect. But, if you added は, it might sound like "Somebody else didn't understand, but John, do you understand?" It works like a "spotlight".
In this case, the teacher is just calling on John to ask the question. So, without は is appropriate.
Is it perhaps ok to put particle は after ジョンさん in the above sentence :ジョンさん、わかりますか。
So I think it is ok to say ジョンさん は、わかりますか。
If I am wrong please correct me.
Note: In lesson "Polite Name Calling: ~さん" it is written:"Who is the sentence talking about? John. Because it is talking about John, we put the particle は on the end of ジョンさん, and place it first in the sentence."