Can the EBow damage my pickups?

The EBow produces a very weak magnetic field. Not much more than the field generated by the strings themselves when a chord is struck. The source of this weak field sits above the plane of the strings, a good distance from the magnets in your pickups. It takes a pretty strong field like that produced by an AC powered soldering gun to affect the magnets in your pickup and even then the gun must be close to the pickup. Here's a great article on pickups at Seymour Duncan.