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.
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