Yes and no, it depends on which kind of calculation you are doing. The basic thing in which sRGB and RGB differ is that RGB is "linear", while sRGB is not. Moreover, the conversion formulas for most pixel characteristics like saturation, HSV value, chroma, luminance use RGB colors, not sRGB encoded (gamma corrected) colors (see Wikipedia).
It seems that PDN has some internal knowledge about sRGB. Because when you e.g. make a printscreen, paste it into PDN and save it as .png, the saved image contains the sRGB flag (ancillary chunk, see Wikipedia). But if you create and edit a new image in PDN and save it as .png, it does NOT contain this sRGB flag, meaning that the image is RGB encoded, not sRGB. (And this is correct behavior, in my opinion.)
And thus I repeat my original question: When I scan an image with PDN, is the image sRGB encoded or not? It should be, I suppose.