The transducer clicking is normal - each click is a signal sent out waiting for a return echo. Especially if you are set to 50KHZ you will hear it click. 50KHz is used for deep water as it has 4 times the energy(and one fourth the number of signals so less definition) of a 200KHz signal used in shallow water.
The return echo timing and wave form tell the computer inside the depth sounder the depth of a return echo and the density of the echo surface. For those who have color sounders, dense objects like rock and salmon give a red echo while not so dense objects like mud or bottom fish give off blue colors. Medium echos like grass or kelp are green (At least that was the colors on the Furuno I am used to watching)
Depth sounder echos CAN affect your fishing. The echo reflects off the bladder and meat on the fish. I guarantee the fish feel the echo ping off them. On a slow day when the bite is NOT on (typical spring full moon where they have been feeding on crab spawn all night) leaving your depth sounder on while fishing will slow the bite down. Look where your line is. If you have a hard drift and the line is a ways away from the boat, the depth sounder ping will be away from the fish you are hooking and it won't matter. On a nice day with no drift and you are fishing directly under the boat (most transducers have 15 or 22 deree cone angles) the ping off the fish will spook them. I halibut fished with a charter captain for years who always turned off his sounder when fishing.
To get an idea of what the return pulse might feel like to a fish, remember the old sub movies where you heard the ping ping ping of the sonar? Each ping is a sonar pulse felt by the fish. My dad was a sonar tech on a destroyer in Korea and they used to chase Russian subs around all day (they were not supposed to be in the "Police Action Zone" with a very high intensity sonar. Constant pinging in the submariner's ears was like Chineese water torture. Same concept. Anyway, that's my