Is there any way to change the style of the DNP marker, for example, to mark a component not with a red cross, but, for example, just make it gray and write instead of the DNP value?
According to the docs, you can’t remove the X but you can change the colour, and the symbol appears desaturated too so maybe use gray instead of red and it might be suitable for you.
DNP symbols appear desaturated and with a red “X” over them in the schematic, as shown below. The color of the “X” is configurable by editing the “DNP Markers” color in the selected colorscheme.
I would like to at least change the thickness of the lines of this marker, they are too thick imho, but it seems it is impossible.
Well, as is, the tech shouldn’t miss it. 
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I do find it a bit obnoxious that an object which is not even on the PCB draws so much attention to it with the big fat red cross, and also that it obscures other properties of the symbol, and I also mentioned this (I think on gitlab) when this cross was first introduced. There are more important things in life, but I still do see room for improvement here. 