My top is decent, but my pads are shot and they look like heLL. I drive with the top down 90% of the time. I figure I would just cut them off for the year. Next year I plan to get a new top. For now I figure it might just flap a bit in the wind when up. What do you think?

I don't see why not!

The top pads help hold the rear bow in place and cushion the top from ripping against the metal frame when you put the top up and down. But if the top is due to be replaced already, I don't see any problem.