Besides taking away from the appearance, I don't think they can hurt anything. IMO
it is just more of noise, and asthetics issue. Also think of it this way, have youever seen a waterfall that didnt make some bubbles when it hits the water. If it bothers you you could perhaps make a small ramp of acrylic of clear plastic that the water can run down rather then fall into the tank. I did this into my sump to quiet the noise and it worked really well.