Another point to make is that testing these devices is expensive. They are low thrust propulsion systems that are designed for thousands of hours of continuous operation. They need to be run in very high vacuum, and for higher power devices there are only a handful of vacuum chambers in the world sufficient for the task. Additionally, Xenon is expensive (dramatically moreso since the Russian invasion of Ukraine), so developing better predictive simulations is critical.
I'd say we understand it about equally well as the weather.
In contrast, the situation with a Hall effect thrust is that we cannot explain a repeatable effect. And that could change with better theoretical understanding. It's in that sense that Hall effect thrusters are "not understood", which I think is a reasonable thing to call it.
(And if you are talking about some aspect of the weather that, unlike the chaotic aspects, is empirically repeatable but not predictable from our models, then I think it would be fair to characterize that as not understood too!)
Aircraft lift is caused by the upward angle of the wings forcing air downwards as the jets move the plane horizontally forwards. This "angle of attack" is usually very small so it's hard to perceive with the naked eye when looking at a commercial aircraft.
Do you mean turbulence? There are some blank spots there but we have very good equations to approximate the behavior, equations good enough for practical aviation.
Basically: We can explain aircraft lift to a college student, but not to a 5 year old. Or, we can explain aircraft lift using equations, but not using informal arguments.
It's about one step away from "We thought scientists knew how rockets worked. You won't believe what we uncovered next"