Does the Steam version of Wonderful Everyday VN have upscaled CG?
Yes, the CG images have been upscaled to 1280x960.

Quoting the official Kickstarter page,


  Furthermore, the English release has been newly upscaled to 1280x960 from the original 4:3 assets, by the same team at KeroQ that worked on the original Japanese release, to ensure maximum faithfulness to the intended product.


Operation Rainfall also confirmed it,


  All of the CG images have been increased to 1280 x 960 resolution [...]


Regarding the black bar, it's because the CG's aspect ratio is still in 4:3 (16:12) while most screens are in 16:9 or 16:10 nowadays. Since the aspect ratio is not the same, the CG won't fit the whole screen and thus letterboxing is used.