I was thinking of composite decking not wooden... But if I have to lower the level I may as well go with natural stone - slate would look nice I think... Won't be for a while though as not as simple as I thought! I wonder how you would get heavy machinery into an internal courtyard actually...
I would think again about decking as it is quite high maintenance. Loads of people are ripping theirs out now. It looks quite scruffy fairly quickly and if you have children running around in bare feet they risk getting splinters in them.
in heavy rain, water will splash up from the ground (or decking) and make the bottom of the wall (or the doorstep or threshold in your case) wet.
It is usually considered adequate to have the ground 150mm below the DPC to prevent the "dry" parts of the house getting wet. You might consider a step.
BTW I strongly recommend having the decking boards running away from your house (not parallel) and with a slope to take the water and dirt away. It is very difficult trying to sweep dirt out of the grooves if they do not run away from the house. The builder will have to know this before he starts setting out the frame.
Is there an issue with putting decking over an old patio so it comes up to almost door level? Would drainage through the boards be ok? It's a small courtyard area and would really improve the aesthetics if it could be decked over!