I used to fly regularly with my cat, taking her on 5 hour flights (when direct) and sometimes a lot longer when there was a layover. My cat wouldn't yowl exactly, but would keep up a distressed meow. I wondered if she would be disruptive too, but I quickly realized that planes are actually very loud environments. The noise from the jet engines is significant, though it is white noise so it is easy to tune out. I'm positive no one ever heard my cat as I could barely hear her and she was sitting right at my feet.
My cat also never eliminated in the carrier. As creatures of habit, it would be very much against their instincts to go on a hard plastic surface in a small space that they can't escape from. You may want to rethink the pad, actually. I put in a kitchen towel once or twice, and it always ended shoved over to one side, she never used it, and it may have just made a small space stuffier.