I am running a whisper filter on my reef tank. Always have, always will. I use the sponges, the tetratech filter pads (not the pure white ones, the white and green ones) and carbon all the time. Water is always crisp and clear! There will always be little trace amounts of things in your tank (from your hands, pulled out of the air, trace contamination in food, the list goes on and on) that the carbon constantly pulls out of the water.
Keeping carbon running will never hurt your tank (as long as you change the pads regularly....like every 10-14 days), and it can only make it better.
As for competing with your LR bacteria, that is ignorance at it's best! There is plenty for all the bacteria in you tank and filter!
I am a fan of Whisper filters. Mine was running on a FW tank for nearly 15 years, and now it has been running on my reef for over 2. Never had a single problem. Only had to replace the rubber gasket on the motor once. If that is not reliable....I don't know what is. In addition, the filter pads are inexpensive, widely available, and a pretty good product.