If the motherboard is properly secured and the cooler is mounted correctly using the supplied backplate and you don't kick the system down the stairs every time there's a BSOD, wouldn't expect any issues. Epxoy PCBs are tough.
Pre-2010 there were many less than optimum backplates and some 1.8+kg coolers and that's when you might have worried.
I've used twin tower Silver Arrows, Phanteks and Noctuas for years without seeing any gravitational induced fatigue - on boards like Sabertooths, UD5s. Most of the cooler's mass is mounted close to the board anyhow.
If you're getting a new board, make sure it's not a thin piece of crap. Cheap boards with heavy coolers with poor mounting systems could be an issue.
That said, for piece of mind, you can consider either cases that offer heatsink support, like some of the Silverstones. Or join the collective cubers that mount the board in correct horizontal position with non-conductive support shims under the backplate. ;-)
And while saying that, there a few smaller single tower coolers that can get within 3-6 degrees of the big twin towers, like the
TR TS140 Rev A with a middle weight of 610 grams. Or the svelte, yet effective (at stock)
Scythe Kotetsu with a feather weight 480 grams. Sure, it's heavy Big Bird feathers, but still...under the Intel spec.
The risk of gravity induced motherboard distortion is lower than the risk of a liquid cooling loop failure pouring liquid onto the motherboard and destroying it electrically.
The Noctua mounting system is very, very good. For me, the overclocking performance and low noise of the D15 is worth the risk of long-term gravitas. ;-)