1) If you keep asking why, science will eventually run into a wall:
"Why do apples fall down?" "The Earth's gravity acts on it to cause it to accelerate towards its centre."
"Why does the Earth have gravity?" "Its mass presence creates curvature in space-time that transforms straight lines into curves along which falling things travel by default."
"Why does mass distort space-time?" "Er..."
The point is that five hundred years ago the FIRST of the questions couldn't be answered.
2)Correct, constantly asking why does eventually lead to a wall. The point is that just because science hits a wall doesn't mean we substitute everything we don't understand with "God did it".
We simply don't have the answer yet and will have to continue to research until we find it. I don't understand how people are satisfied with just saying god(s) did it. We can always strive for more knowledge.