There is no noticeable difference in performance or price between the NH-D15 and the NH-D15s.
The benefit of the s is that it is a tad better for compatibility since it is 5cm shorter which is not an issue in your case.
The s is offset because some graphics cards mounted in the first pcie x16 slot will have backplates that are impacted by some coolers.
There is a very big difference between the i5-9400 and the i5 9600K.
The latter can be overclocked to 5.0 and is a much stronger processor.
Have you shopped for a smaller M-ATX motherboard like the ASUS Prime Z390M-Plus ?
https://www.amazon.co.uk/ASUS-Prime-LGA1151-Gigabit-Motherboard/dp/B07HRWN6TH/ref=sr_1_3?crid=QZMPO7895EME&keywords=asus+z390+motherboard&qid=1552863164&s=computers&sprefix=asus+z390,computers,236&sr=1-3&th=1
The main difference is that M-ATX has only 4 expansion slots vs. 7 for a full ATX motherboard.
Past the graphics card, just how many might you ever use?