I can't really tell about Gintama as I didn't see the anime or read the manga, but with SNK I watched the first season and jump straight to the manga.

The first season I truly enjoyed watching but with the second and the third I feel like I know the plot, but the action scenes are truly well driven and exciting. So I will say that a mystery theme story is probably better to watch it first rather than dive into the manga/novel.

Another thing that comes into my mind is that when you read the story you actually imagine it, so it is not tied to someone else's work, it is as u wish it would be.

(Sorry if my english is rough, not my main language :P)