I'd been using exoshields just because I don't like rebuilding the harvesters. You can't rebuild the harvester as soon as it is destroyed, you need to wait until the enemy moves away or is eliminated, and my harvesters were having a lot of down time before I remembered to do that.
When the resources are shielded, the command center is like a magnet for the AI ships. This is great for drawing them all to my turrets when there is no choke point (The wave can appear from several wormholes, and there are multiple wormoles to adjacent systems of mine). Actually, why does the AI hate command centers so much? If the command center is providing supply to something vital, it is important, but otherwise they're fairly cheap and easy to replace.