Hey there.
I think you are onto the main problem, which is resonance, a sharp build up at a particular frequency. I'm always notch EQing them down because they will remain annoying otherwise. A dynamic EQ can be useful, but regular notch works of course. Beyond that, how I would EQ a drone depends what is sitting with it, and where it is good to leave some space for other sounds. For which there is no real formula. Drones and pads can vary greatly, so it is more a case by case issue. One good trick is to turn the thing up loud. Does it still sound balanced and listenable.
Often I will EQ a drone to shape its spectrum. Lower some frequencies and bring up others ... maybe to add a bit of brightness to the high end or cut the boominess in the lows. But as I say, on a case by case basic.
As you say, getting it right when selecting initial sounds and layers is very important. But in my experience some EQ will usually be needed to balance things later on. EQ is such an important weapon.
Because our ears and mind get tired and a bit untrustworthy, I will always park a finished piece for a week or so, then come back and listen it more objectively, as though it were someone else's piece. And listen for anything annoying. Then try to correct it. This will primarily be an EQ job, and some related volume balancing.
Conclusion : For me there is no one way a drone (or pad) is made or should sound. But there are technicalities and aesthetics of music that should be observed. Which means: It should sound good. If it doesn't it needs work !
