Lightning surge protection advice
I have repaired 2 homes that had lightning strikes 1 was direct and there were breakers all over the house (it burned the bus was even partly melted) the second one was an indirect strike. The damage to the electronic components is due to the high voltage more than the current. With that said surge suppressors clamp the voltage until they overheat and fail. 

A whole house surge suppressor in your main panel may have helped if it was large enough, the second house that was a indirect strike was protected by a suppressor that could handle close to 30 amps. The suppressor was toast both elements failed but they only lost 1 TV set that was on when the strike hit. 

How surge suppressors work: 

Most are metal oxide varistors. These devices conduct once a voltage threshold is reached and dump the excess voltage to ground the voltage threshold on some that I have used range from ~260v and higher close to 800v. 

in the U.S. the maximum voltage voltage to ground is 120v rms for residential. 240v is leg to leg but the maximum potential to ground is 120v rms so you want a MOV that breaks down in the +200v range. 

Next is the amount of energy that the mov can conduct rated in joules. Once this value is exceeded they do fail. Whole house units usually have led’s that show if the elements are working, some are replaceable. 

As you found out the one on your pump failed it tried to do its job but was not large enough. I suggest putting the largest one you can afford at your main panel. 

I usually install these because of industrial loads causing spikes and damaging electronic equipment. Oregon is not known for its thunder storms and having seen 2 strikes is very rare here. 

I can say nothing will stop a direct strike but an indirect strike or industrial loads and power line switching all generates spikes that can do damage by installing a 300$ or larger surge suppressor may save many times its cost over its life there are smaller ones for under 100$ these are very limited on the size of the spikes they can handle and some that cost close to 1000$ these monsters can almost take a direct strike.

I have found the ones that require a 30 amp breaker to be the best value for my area and they do not fail very often where the smaller ones do fail more often so in my opinion going with a larger unit will provide better protection and possibly last forever unless a close strike. 

So why did the breaker not trip? 

It could have been the current / duration was low enough not to trip but the voltage did the damage. This is where whole house surge protection pays off just make sure to get one that is large enough to handle the spikes that may happen in your area.