It's unlikely than a small amount of beaded water on the top will damage anything, but like
@miko1aj says, it's not a good idea. If you have a lot of rain or dew and this is a problem, here's an option. Go get some Rust-oleum NeverWet for outdoor fabric and use the whole bottle on your canvas. Put Rain-X on the rear glass. Now, if the top is wet, all you need to do is drive for a minute and all the water will be gone. One word of caution, though. The NeverWet is so good at making water not stick to the canvas, when you get in and out of the car and there is beaded water on it, be prepared to have it all roll off the canvas and onto you!