Would be interesting to see a poll on which is worse - slightly blurry "square" pixels, or slightly non-square "perfect" pixels. At a glance, I immediately noticed how blurry the shader's pixels are, but it wasn't until reading this blog post that I even thought about the problem of fractional scaling for pixel art games.
Worth pointing out that most SNES games had a vertical resolution of 224 pixels. At that size an upscale for a 1080p screen results in a maximum pixel irregularity of 1/5 (most pixels are 5x5 with the occasional 4x5 and 4x4 pixels thrown in). That might be close to negligible on a moderately high DPI screen.
Interesting side note about modern pixel art games: Celeste has a native resolution of 320x180. That's almost exactly the same number of pixels (or scan lines) as a typical SNES game, but the number is chosen to divide evenly into 1920x1080 (and 1280x720), meaning that you can get perfect pixels on common modern resolutions without fractional scaling. Kind of brilliant, actually.