I seem to be having issues with cones in my cheaper wheelsets. So, if you're really pounding out the miles, something like Ultegra may well be a good choice. Or, as mentioned, some even more boutique hubs.
I'm not sure about tires. I've commuted on tubulars (sewups), clinchers, and now experimenting with tubeless.
I suffered my first catastrophic tubeless failure last weekend. I did get myself back on the road eventually, but lost a lot more time than if I had simply gotten a flat with a tube tire.
I started this thread a few days ago:
Durable 25mm Tubeless? "Training Tire"?
A couple of people have suggested
Pirelli Cinturato Velo TLR as a tire for puncture resistance, and reasonably low rolling resistance.