It might be that the image is thought to relate to publishers' ink, the ink of the printing press. But is that ink actually ever spilt? The "spilling" of "ink" evokes the image of the fountain pen, and a pot of Quink, but perhaps that is just me.
I must admit that it is not an image I like to use. It's a scholarly cliché that's used to express frustration at the extent of the literature on a topic that one feels obliged to deal with but wishes one did not. "Much ink has been spilt on . . ." means something like: "More has been written on this topic than I refuse to read".
Still, I wonder what will have replaced it in a century. "Many megabites have been wasted on . . . "? "Many keyboards have been worn out by . . ."? "Many a neural interface has malfunctioned on . . ."?