Personally, I don't walk when there are lightning storms. Certainly not in the mountains, or in high flat areas like the meseta, and especially not when there's long stretches without possibilities to stop early or seek shelter.
Most other pilgrims seem to just walk through them and hope for the best. It's unlikely to be struck by a lightning, but up in the mountains and in areas where you're the highest point around, there is a higher risk. What one does with that knowledge is personal decision.
I'm likely to die from a heart attack out of sheer panic
so I avoid such weather.
In case of a short summer storm, I seek shelter and wait (always good to have a look at the sky from time to time, then stop somewhere in a bar or a church before it starts). Sometimes I cut a day short (summer storms usually don't start before midday). When walking in the alps, where storms in the afternoon are common, my goal is always to have arrived before noon. Same elsewhere when storms are in the forecast.
Yes most summer storms are short, but that's not always the case. Last year on my walk through France, there were several days with storms that just didn't want to stop and went on and on. Once I had to knock on a farm's door to ask for shelter in the afternoon, because I couldn't continue for the last 10km to my campsite, and the storm only stopped in the morning (it had not even been in the forecast!). The next day a lady in a shop down the road showed me pictures she took in front of her shop after a recent storm. The ground was covered about ankle deep in hail the size of pigeon eggs...
I wouldn't want to be stuck up on the Napoleon route in really bad weather, certainly not a nasty storm with hail, strong winds and all. It is not at very high altitude, that's true, but there's not much protection from the weather there.
The Valcarlos route is beautiful, too, and has a good municipal albergue at the half way point that is likely to be quite empty at this time of the year, and where you can stop in case of the weather getting bad.
With a stop in Orisson/Borda though, it's likely that you'll arrive there (as well as in Roncesvalles the next day) before the bad weather starts.
As the others said, definitely ask for advice in the pilgrim's office. The mountain weather can change quickly. Maybe the weather forecast changes and you'll have wonderful weather, it's all possible.
No need to worry too much, just be flexible with your plans and adapt to the advice given by the pilgrim's office, as well as your gut feeling.
Buen Camino!