Non-rev refers to any non-revenue passengers. You're conflating NRSA (non revenue space available) with non-rev generally. There's also NRPS (non revenue positive space) and "must ride" flyers in that category. This flight was picking up airline personnel, not revenue passengers.

Your having lived through hurricanes on the ground is entirely irrelevant to a discussion about the safety of overflying the hurricane.

At the flight altitudes of a commercial jet none of the effects you mention happen. You need to plan your path carefully for the descent, landing, and takeoff. But at cruising altitude, hurricane winds are not a major safety concern.