Currently there aren't any proper mods for Shovel Knight but there's a couple things we can do regarding the game's sprites. I was able to find a tool in C that can read and convert/extract those from the game's proprietary format into PNG sheet form, which leaves me wondering if the reverse process is possible -- saving spritesheets back into the original files (which would allow visual mods).

Unfortunately my coding knowledge is very basic so I can't do much in that front myself, but at first it would consist in having a look at the tool and figuring out if the process is reversible in any way. If anyone with programming skills has any interest in helping out, please let me know and I'll hook you up with that stuff.