The pass is safer than the peaks on either side of it, but less safe than not hiking over the pass.
When I did my Instructors course for Summit Adventure, hiking over a pass during a thunderstorm would have been considered extremely unwise, and the procedure would have been to either not cross or to get the heck off if you were on top and saw a storm coming.
When I did the Uinta highline trail last summer, there was basically a pass to cross every day, and plenty of thunderstorms. I just waited the storms out in the valley below rather than risk it.
You want to have enough leaway in your planning that you don't have to cross the pass right then and there.
Same for ridgelines, you want to be heading down if a thunderstorm rolls in.
As for estimating what taller points are more likely to be hit, there is a What If XKCD on the subject.
