changing the water frequently and in large amounts when there is ammonia or nitrite present in the tank is what keeps your fish healthy and happy. ammonia poisoning isn't pretty, and nitrite can affect the blood - essentially blood poisoning.
changing water on a regular and consistent basis in a cycled tank keeps the water parameters in check - nitrates, TDS (total dissolved solids), and DOC (dissolved organic compounds). these three things are what can cause a tank to go downhill in the absence of maintenance, not just nitrates as some people think.
the only thing you do when you remove old water is remove the food source for the bacteria, not the bacteria itself. the bacteria stay attached to surfaces and are not floating around in the water at all. when you have fish in the tank, they are constantly creating more ammonia, so the amount of ammonia you are removing during that water change will be replaced soon enough by the fishes waste, and the bacteria won't be long without 'food'.
you can do a water change without doing a gravel vacuuming, if there isn't much mulm in your gravel. gravel vacs are meant to get rid of all the decomposing crud in the gravel, so that it doesn't foul the water or become a 'nitrate factory' (lots of mulm buildup causes increased ammonia, which in turn causes more beneficial bacteria to be produced, which in turn causes an increased end result of nitrate) <-- the bacteria will only populate enough to handle the amount of ammonia being created in a tank, so you see where i'm going with the excess mulm talk, eh? keeping your filters clean of excess mulm buildup is also good to avoid this 'nitrate factory' problem.