The current design is to have the game remain 2D in a 2D space with shallow shadows as if the Sprites are paper cut outs sitting just above another layer of paper. However this presents a stack of challenges.

Option 1. Draw all the shadows into the sprites. 

Not only does this create a ton of extra work, When the sprites, Player and NPC's overlap upon attacks etc. the shadows cross over layers and does not look good at all. Plus I'm going for more of a 2D style of what was achieved in 'Paper Mario' however Paper Mario was built in a 3D space. 

Option 2. Draw shadows as a separate sprite sheet.

Again a ton of work and not sure how easy this would be to implement without bugs and may increase CPU load. The project is designed to run on even the oldest machine so this isnt a good option. 

Option 3. There appears to be 2D 'fake' shadow options built into Godot.

This will require more investigation but looks like a good option.
2D lights within Godot 

also a better option may be 

To use code to make a copy of each sprite, colour black, and add to a single layer behind the sprites. This will require testing. 

NOTE: you think your game idea is simple until you start actually working on it and realise there are hundreds of elements you didn't think about.