Emm... He HAVE? Not Has?
No. It is a question with the "did".
In English, it is "he has" in a statement in the present tense. In a statement about the past, it would be "he had." But in a question about the past, it becomes "did he have."
The Czech verb is in the past tense (MĚL). "Have" is appropriate in the translation.
Add "Did he have problems with his both knees".
Nope, that one doesn't work. But "both his knees" and "both of his knees" are accepted.