Tom
In my experience the Hasselblad implementation of the Kodak 39MP sensor is certainly prone to colour noise. This, of course, is something which is particularly noticeable in areas of plain blue sky, but the noise is there in the rest of the image too. Having said that, I find that when shooting at ISO 50, as you are, the files really are pretty good straight from the RAW. I do a lot of handheld stuff at ISO 200 and even 400 (in the winter) so then it becomes more tricky.
I do not use Phocus, so I can't comment on that, but I find the noise reduction in Lightroom 3 and higher to be really excellent at dealing with the colour noise. Usually an amount of 20 to 25 will remove it, with no effect on image quality other than a positive one. If you have a plain blue sky then mask it when sharpening, of course.
John