McKenster Welcome to our friendly cabin on the good airship PPRuNe.
We can be lively but please don't turn in your ticket too quickly.
As Dash8driver1312 says, you can never be 100% sure what a piece of 'empty' air will hold - because it ain't empty. There are weather radar units that are very good at showing where water vapour is - and the turbulence involved with it - but air of different pressure zones does not show up, unless there are extreme conditions. The good news about aircraft is that they are designed to take considerably more than your 'pooper' can! If the conditions are uncomfortable, the flight crew will be looking for a route away from that patch.
That said, the usual passage of an aircraft in ascent and descent will be moving rapidly through the layers of air and cloud and will usually 'run out the other side' before any direct action is needed.