So I'm driving back from Wyoming this week, top down soaking up the rays until I reach the mountains here in Colorado. It clouded up, but I thought "no worries - NAM writers say you don't get wet". After 10 minutes of a real gully-washer I was soaked . The inside of my windshield was wet and fogged, my dash was wet, back seats, passenger seat and me down to my waist - dripping.
I have the Wet Okole seat covers so I wasn't concerned about them, but my stereo was wet so I turned that off. I drove through the storm at 45 - 60 mph (would have been faster if I could have seen better) with the windows up, down and in between; the windscreen up and down - nothing seemed to make a difference it was like I was driving under water . Jeeze!
Then the sun came out and my Mini and I air-dried together and all was forgiven.
So based on my experience (at least in a real heavy thunderstorm) top goes up in the rain .

 

My experience is that 60 mph is an absolute minimum to keep dry . .. the bigger the drops the faster . . . . It isn't always wise to speed up in the rain, and on a busy road there may be cars in front of you which don't speed up. I've dived for the next overpass in those conditions where, unlike the motorcyclists also seeking shelter there, I scoot off again after the top is up.

Most of my thunderstorm experiences involve briefer, lighter teasing rainfalls. I keep the top down until I am forced to put it up. The sky is so beautiful before it falls on you!