Yes, these things do happen.

The pump down a well provides a wonderful ground for a lightning strike and a direct or near-direct strike (or, say, a strike on your nearby power lines) will look at your pump down a well as a wonderful path to ground. The strike's voltage will easily punch through the insulation on the cable going down the well, through the insulation on the pump motor windings to the case of the pump, etc.

It it happened to both pumps at the same time, my first SWAG would be that you had a strike on your power lines somewhere nearby.

About the only thing you can do is put a lightning arrestor on your pump breaker panel and a nice ground system right there at the panel. Check the arrestor frequently. Some of the arrestors I use self-destruct in a strike, allowing the panel/pump to continue to function, but now leaving you without protection for the next strike. Even an arrestor and ground at the panel is no guarantee that lightning won't take out your pump & wiring in the future -- it only reduces the chances.