Z Siege Engines are basically the Coke version of a Pepsi Plasma Siege Engine. In addition to a more favorable ship cap, they've got better speed, damage per shot, and armor type. The cost is less overall health and firing speed. Key defense is to keep them moving, because it takes 10 seconds from when they stop to fire their first shot. Kiting with fighters is highly effective.
Best static defense is sniper turrets (both flavors) and time. If they're going to pop out of a wormhole right next to your guard point, you've got a major problem. If you can force 'em to fly for a bit (doubly so if they're hitting a logistics post), you can whittle them down and burn out their engines. Focusing the snipers to fire on their type (ctrl+rclick one of them w/ the turrets selected) will generally help. If they get up close to the forcefields, pull the engies/rebuilders out from under it like you would for a normal siege engine defense.
Generally, I only hack a design backup if the AI is actively using that ship type in an annoying way. I may be over personifying it, but the AI seems to play like it has an ordered preference list on which ships it buys additional ships for reinforce or other similar events. The list seems to also randomize with each game, so if the ship type isn't popping up high on the list for this game, it probably isn't worth the HaP to remove it until the AI gives you a reason to.
Full disclosure: I prefer coke to pepsi.
