Thank you for you’re detailed response and sorry for my late reply, I’ve been busy these days. I tried what you said but got the same results. I tried with a photo taken with Neutral Picture Control and Active D-lighting off but Capture NX-D generates two color profile files, one with weird colors and another “unsupported” on darktable. Changing the Picture Control and turning off AD-L in Capture NX-D has no effects in the color profiles. I also tried several color spaces (Nikon sRGB, Adobe RGB and IEC) and made sure the “use this instead of” option was checked. Also, the files are a lot bigger than the ones for the D3100; about 1.6MB each.
I’m starting to think that photos from the D5600 are processed in a slightly different way incompatible with darktable. I’m going to keep trying with different settings, though.