For pixel art games, there some things you have to take care of:
1 - Reimport all your textures without filter, or with "2D pixel" preset. Just select the textures in your file system dock in the editor, go to the Import dock, uncheck filter, and click reimport.
2 - In project settings, go to Display->Window and select "viewport" in Stretch mode (at the bottom of the dialog). This makes godot render at the window resolution and the scale the result, so you only see what was intended, and the performance is a bit better.
3 - In the same Display->Window settings, select "keep" in Stretch Aspect option.
4 - In project settings, go to Rendering->Quality, and look for 2d, check pixel snap there. This makes things snap at integer pixel positions, to help you avoid subpixel distortion.