There are two types of PCIE lanes. 8 lanes run off of the PCH (chipset) and 16 lanes from the CPU. If it's a PCIE gen 3 slot, it is running off the CPU. Motherboards generally also have a PCIE gen 2 slot (or sometimes more than 1). If it is a gen 2 slot, it is running off of the PCH. PCH and CPU slots don't interfere with one another. I'm 99.9% sure your x4 storage device will not affect SLI speeds. You should be fine. But you should state your motherboard model to be sure.
Basically, that means that the SLI slots will run off of the CPU pci express lanes, and the x4 storage device you're using will run off of the PCH. The chipset (PCH) lanes and CPU lanes are separate. Therefore, they will not interfere. This is how the vast majority of motherboards will work with very few exceptions, and like I said, if you can name your motherboard specifically it can be verified. But there are very rarely instances of an x1/x4 slot interfering with SLI pci express slot speeds. That is very rare unless the board is just poorly designed.
edit: you also mention the 3rd slot is gen 2. If you say the 3rd slot is PCIE 2.0. That means it is DEFINITELY running off of the PCH. So it will not interfere with SLI. The upper 2 slots will be the SLI slots running at x8/x8 and you can put whatever you want in the PCIE 2.0 slot - if it is a 2.0 slot, it *IS* running off of the PCH which means it won't interfere with SLI speeds.
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