1. Can you build WMD on your home planet? Seems like it should be no as there is no way to attack them there
You can't attack a home planet with WMD but you can still land population on an enemy home planet. The owner of the WMD is the player with the most population cubes on the planet (even if the planet in question is another player's home planet)! With that in mind there is no reason why you wouldn't be able to build WMD on your home planet.
2. The shield tokens are 2 sided. If you buy a number of magnetic shields, then later you want to upgrade to MPG or QGP shields and the high council board is exhausted, are you allowed to flip your magnetic shields to their alternate shield identity? In which case you would need to plan ahead when selecting magnetic shields, seems a bit messy
A player can discard upgrades when ever he/she wishes to do so. So, the way I see it, nothing is stopping you from discarding a shield before buying upgrades then buying the same component again for the other side, essentially flipping the component. I agree that this seems a little messy. This is not the only part of this game for which the components don't live up to the game, especially if you have the first edition...such a shame