Ki2is87
Hi, 
 
I´m using just 1 graphics card.
2 m.2 slots of my X299 FTW K board are already populated with 2 970 evo plus 500gb drives.
I´m planning to buy a ASUS Hyper M.2 X16 PCIe 4.0 x4 riser card and populate it with 4 M.2 980 pro 1Tb cards. 
 
According to the manual, it should be possible to populate 2 x 16-pcie3 slots.
So that means, I can put 6 cards in total, 2 on board and 4 on the riser card, right ? 

You should be able to as long as you have pci bifurcation enabled. If bifurcation isn’t enabled, you won’t be able to see all 4 drives.

I do not know if the BIOS for the x299 Dark is similar to the x299 FTW K.  I just tested my Asus Hyper x16 PCIe v2 on my x299 dark and successfully booted from it with 3 NVMe drives in it all of which properly displayed in the BIOS and in Windows.  I set my PCIe SSD setting to "PCIe SSD Card (Non-VROC)".  I also set the PCIe setting to "Gen 3.0" instead of "Auto" just to be sure it was set properly.
 
If the CPU used features 44 or more lanes, it should work, assuming all of the slots on the Hyper x16 PCIe v2 are filled (requiring 16 lanes).  So the count would be 16 for GPU, 8 for two native m.2 NVMe drives, and 16 for a full Asus Hyper x16 PCIe V2, totaling 40 lanes, leaving 4 lanes something else.
 
EDIT:  O.k. so after perusing the x299 FTW K manual, only one M.2 slot (the 110mm slot) is set for using x4 CPU lanes.  This means that the OP's second M.2 is running on PCH lanes (thus slower).  So I guess this would leave 8 lanes for other stuff instead of 4.