You can also right click on the render window. Blender will serve up pixel values with and without colour management, as well as hue saturation luminance and a little swatch.
I didn’t know that. Nice.
Blender is showing (0.00000, 0.00000, 0.00000) values wherever I click. This is further evidence that the problem is occurring later, most likely during conversion to PNG.
Couldn’t confirm exactly how it happens, but I would guess either in the conversion from 32-bit float to 8-bit integer, or during compression, there is some rounding. Saving as 16-bit allows more digits after the decimal, so it can use all the zeros to compress and approximate zero. 
I would hope that Blender is not rounding (0.00000, 0.00000, 0.00000) to (1, 1, 1), even with 8-bit integers!
Krita shows the 8bit png as clear black 0,0,0 but the 16bit png is all one bit off true black.
I haven’t tried Krita myself, but this is indeed weird. I can’t imagine why different programs would report differently the colors in a single PNG file.
I would look at some of these comments about the issue being on Linux because I can’t replicate the issue in blender on windows but I also haven’t pulled open your specific file yet. I’ll try it when I can get to my computer again
Thanks. So far, it does appear to be a Linux vs. Windows issue, probably in the PNG-writing library or Blender’s use of it. I just tried EXR, and both Float (half) and Float (full) produce pure black, as expected.