Probably bad and potential root rot. It'd look like a plant you have over watered every night. (Ok not exactly but you see what im suggesting). Im all soil and never done "hydro" though. More answers may come from hydro growers.
Edit:
http://m.ebay.com/itm/New-25X25X5CM-Studio-Acoustic-Foam-Sound-Absorption-Treatment-Panel-Tile-Wedge-/252345808139?hash=item3ac0fb750b:g:O1wAAOSwWBJXBNNy
You could measure out your pump in centimeters and get a couple of little soundproofing squares. These in the link above are less than $2 a pieces.
Is your pump hanging? Pic of setup? My 951gph air pump roars in the room i use it in but is suspended from bungies and does touch anything. I brew conpost teas for 24-48hrs at a time. When i leave the room i cannot hear it.
http://m.ebay.com/itm/Air-Pump-Commercial-951-gph-Elemental-O2-Aquarium-Hydroponics-Aquaponics-Pond-/371573724091?txnId=815098630024
Errr oh yea. Ebb and flow might allow for off periods im not positive they can run off an air pump but rather a water pump. The plant sits in a top reservoir with a bell syphon and water is fed crom below into the top. It fills until.the water level reaches the top of the bell and a naturally occuring.vacuum pulls the water back down. Repeatedly..
The roots wont be sitting in water if this system is turned off while the top tank is empty. Itd take calibrating with a float switch but that's pretty easy to manage if you have a plan. I say this because if turned off halfway full the water will sit until the pump comes back on. It'd need a digital AND gate saying "when the float is low and the timer is saying to turn off, then i can turn off" ya dig???