Yes, it depends on the gun design. The two basic types and bent gun and slant cut. As near as I can make out, the bent gun uses a single magnet and the slant cut uses a dual trap.
I agree with what notimetolooz posted earlier. You're not going to cause ion burn by a misaligned trap but you can damage the gun elements with the electron beam.
Here's a diagram of how the double magnet type works.
