In general, you need a lot more than a cube to decide a scale (not just for Godot but for 3D in general, and 3D units are not pixel).
The screen, the camera (frustum in particular), the size of your playable zones, the relation between small and big objects, and more…
Like, if your cube is a Borg cube, one unit will need to be a lot more than 1 meter but less than 1:3000 if you want to add a lot of small details to the game.
And for textures, you can squish a 4096x4096 texture into a 0.01 units cube and may look like a pixel from a regular distance, while a 1000 units cube and a 64x64 texture may look fine with the correct setup.
Textures define details, on a 512x512 you have double of pixels than on a 256x256 one (double per line, 4 times in total), depending on many factors it may look better or not and affect performance or not.