If the ion damage hasn't cooled off, getting hit with more ion resets the timer - that way it can build up over time to take down the shield system entirely, regardless of how many shields there are. A string of misses can ruin the fun (more on the higher sectors), but because of the high firing rate your weapon guy will increase in levels quickly and reduce the chance of that happening.
I haven't had humongous success with the Noether. Against some opponents, the Zoltan Shield is enough, but against other Zoltans and in asteroid fields you will suffer. That said, the weapons are excellent; you just need those 100 scrap fast.