A second issue to check is that the unconnected overhanging part of the video card may possibly collide with capacitors or heatsinks, so check for this before you start cutting into the PCIe slot or the video card.
Any board/component collision problems can be solved by completely cutting off the card edge pins that won't be connected to anything, though this risks damaging the multi-layer circuit traces in the video card.
Though in general the concept is sound. PCIe will use all available lanes so you can theoretically still get at least 8x performance out of a 16x video card.
Also, you might be able to find an 8x to 16x riser card, designed to work with low-profile video cards. Some Google searching turns up this possibility: