With a very low-end card like a 730? Yeah, it wouldn't make an appreciable difference. Especially with an Atom CPU - you're going to tend to be CPU bottlenecked almost no matter what you do.
With a low-midrange card (if you wanted to pick up a used 650 or the always-popular 750Ti) I'd believe that the 1x lane might bottleneck you vs. 2x lanes. But again. Dat CPU.
Still, that explains why it's got a 2x slot - that's typical for storage controllers (2x for the low end ones and 4x for the nice ones.)
But you'd almost be better off selling that board (could probably get $100 for it, it is server hardware after all) and buying a
desktop-oriented MB/CPU combo with a larger PCI-E slot.
Or even stretch the budget a bit and get an H81 ITX board with a Celeron 3xxx series or something. Should set you back around $120 and would have a no-joke x16 PCI-E slot.
Likewise, an A8 APU and an FM2 motherboard (if you're an AMD fan) would be around $150 and you wouldn't even need a graphics card anymore.