M.2 SSDs tend to run warm because they have little surface area and are isolated from airflow and are unable to conduct heat into surrounding material as they only connect to the board via one screw and the small M.2 connector itself. Any air flow, even if it's well above ambient temp, will cool them. If no air flow is possible, just stuffing a thermal pad (or stack of thermal pads) between the controller (and any power delivery on the M.2 card) and the motherboard will usually cool them well enough to completely prevent throttling. No M.2 drive produces significant heat, they just get hot because they have so little cooling.
Most M.2 drives will run warmer than the air coming off a heatsink, even while the CPU is at maximum load and the SSD is idle. With even light air flow, the air leaving a good heatsink will be less than 10C warmer than the air going into it and if it was blowing at an M.2 the SDD, it would cool the SSD. Any air flow that is cooler than the component is going to remove heat from the component. A 25C ambients, 30C internal case temps, and ~200w of heat being dissipated by the D15S on my 5820K, the air coming off the heatsink is never hotter than 40-45C. If the SSD is 50C, 45C air will cool it down. Most M.2 SSDs won't throttle until ~80C.
There also isn't going to be any significant radiative heating of the SSD, again because the temperature of the heatsink is probably lower than the temperature of the SSD, and radiative heat dissipation is very poor at low temperatures anyway.
Also, the side fan on the R5 doesn't quite fully overhang the first PCI-E slot and the NH-D15S generally doesn't reach below the the I/O panel. Even if the D15S was tall enough to interfere with a fan above it, that's not where the side panel fan will be in the R5 (and yes, I have an R5).
How I cool my M.2 SSDs:
Just sticking the thermal pad stack under it knocked off ~30C.