Glass can have a coating on it to reduce reflection, just as you have on many camera lenses.
Ideally the whole system may need to transmit 99% of the light to be effectively invisible, that would have to be tested. If the plane is moving that also makes it harder to see,
The embedded magnets idea would depend on how many magnets are needed and how much they would block light. For example the same effect might be done with small electromagnets which could be stronger. I don't know if it's a viable way to do it, but it works quite well for mobile phone radiation. No doubt it also depends on the wavelength of the radar. I don't get too deeply into that side of it, it's the sort of thing that would require a big budget to test.