Welcome!
The nanoKontrol is most likely NOT the cause of the alerts, but the symptom of what the alerts are telling you. It may seem the nano is triggering these, but in fact, it is probably only exacerbating how your system is struggling to keep up. Some sample libraries demand a lot from your CPU.
Your audio buffer sizes may probably be set too low in Logic Pro X, so I would check there first. Sometimes you have to experiment, gradually raising it until you quit having issues:
https://support.apple.com/en-us/HT203930
To ask the obvious, how much memory do you have installed? That too can be a factor in handling sample libraries, though you may already be aware of this.
As for sample libraries like Spitfire in Kontakt, there too you have to optimize Kontakt’s settings to find that sweet spot while you work:
https://support.native-instruments....-Can-I-Optimize-the-Performance-of-KONTAKT-5-
It’s about four years old now, but this overview by Impact Soundworks is useful also:
https://impactsoundworks.com/optimizing-your-kontakt-workflow-part-1/
As for the nanoKontrol, that kind of data output can easily be smoothed out if you trace back over it with the pencil tool. Sometimes, those points are all being generated because you are not turning the knobs (edit: or sliders) fluidly enough, and with something small like the nanoKontrol, there is only so much you can do, short of trying something else with a bit more of a throw. I don't have the nano, but in its editor software, see if there is a way to adjust the interpolated hardware sensitivity.
Finally, how many mic positions are you loading with the Spitfire library? Each mic you use loads more into RAM, and increases the load on your CPU, relative to your system specifications.
Greg