I don't think the weather is a good analogy, at least if you're just referring to the unpredictability that comes from chaos. That the weather is unpredictable

I don't think the weather is a good analogy, at least if you're just referring to the unpredictability that comes from chaos. That the weather is unpredictable (when projecting out a few multiples of the relevant Lyapunov time) is an unavoidable consequence of chaos. Indeed, if you could hypothetically run a full atomic-level quantum simulations, the wavefunction would contain different branches where different weather events happened; there is literally quantum uncertainty in the outcome, even if we had a complete theoretical description and understanding of the different outcomes. 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!)