Almost all dual port copper (RJ45, Cat5, Cat6, etc) Ethernet cards operate as independent interfaces, meaning that the Operating System and any software involved doesn't really notice that they happen to be sharing a slot on the motherboard. At least as far as you or any software you're concerned about cares. If you happen upon a card that doesn't operate this way, then it's most likely some oddball card that wouldn't be supported anyway. If it's in the supported hardware list, it should operate in the way that you want.
The main point that some people don't notice when starting out, with optical cards, mostly, is that it takes 2 strands of fiber to facilitate communication on a single port; what may look like 2 sockets is still a single port; one side sends, the other receives. The other side to optical cards is them not being obvious by appearance as to whether they're an Ethernet card or a FiberChannel HBA. Look up the model, it'll tell you. There are dual port Optical cards as well, both as Ethernet and FiberChannel. In the Ehternet realm, dual port Optical cards should operate as 2 independent interfaces; FiberChannel, not always, but that probably doesn't fully matter for your purposes.
Oh, and there's also Quad port Ethernet cards. Those should also be 4x independent Ethernet interfaces.