Da Vinci had not calculated anything regarding the cosmological microwave background and all of that. This is much more recent. This being said, Da Vinci was a great man.
To answer the other questions: the equipment is built to resist the flight. No damage has been found after this mission and data is being analyzed at the time we speak (or write). This is however clear that damage can occur, even with all the undertaken precautions. For more information, I recommend having a look to the Pilot webpage I am referring to at the end of the post.
Well, after reading some dan brown books, i cannot think that there is an unknown aspect to his inventions.
I do not question his knowledge about measurement background etc. , but don't you think, he knew, that the day will come, when those balloons will reach greater heights and be helpful for mankind?
Ah ok, I misunderstood your comment. I thought you were discussing the astrophysics side, which Da Vinci was most probably unaware of. For the balloons, I don't know whether he has thought about such balloons (I really don't know), but that is possible/ Knowing the guy... :)