I'm at a point in the game where I really don't need the materials from downed UFOs. I know there are penalties for not shooting down UFOs, but are there any penalties for shooting it down and then declining to assault it?
There are no penalties.
The panic will not change, and that is all that matters.
You will still get an A on your council report aswell.
I have confirmed this on Ironman Impossible, as I choose to ignore a downed battleship, and there was no negative outcome.