A curious question! I think the pci-e version used would probably depend on the motherboard.
Several things
1) If this is a NAS it should be low powered. Newer graphics cards are more power efficient. Maybe consider picking up a low end 5K series ATI card. They are inexpensive and are certainly pci-e 2.0. So that solves the issue outright.
2) Whilst some motherboards have 16/8/4/1 size pci-e connectors it certainly does not mean that they are going to be used at the level you expect. For example, many motherboards will make 16x slots run at 8x when two PCI-e 16x devices are used. So check your motherboard manual to see what happens when connecting multiple pci-e devices.
2) Say your old GPU did force the raid controller to run at 1.x. An 8x pci-e 1.x should be able to transfer 2GB/s. My Areca ARC-1880i, a hardware raid card, had a maximum read at something like 2.3GB/s in a benchmark I ran. Just for reference the average read was 176MB/s. So unless your card is going to run at 2GB/s constantly you aren't going to saturate the PCI-e bus even at version 1.x