It's best to stir the upper portions of the substrate and vacuum the top. When that's done only ammonia and nitrite consuming bacteria live where the vacuum can get to them. The bacteria responsible for eating nitrates live either deep within the sand bed or inside the live rock where there's no oxygen. Cleaning the substrate will remove detritus before it breaks down and releases waste into the water. It also serves to extend the life of your sand bed.
Changing your water is the best way to remove nitrates that are already there. If you're having a problem with nitrates building up in the water perhaps a review of your setup is necessary. A setup where no nitrates are present requires that virtually all of your nitrifying bacteria live in your live rock or sand. If you have another filter, even something as small as a sock or filter bag full of carbon; if not replaced regularly they can serve as a biological filter. When that happens they create nitrates that aren't removed by your rock and sand. Only nitrates created within that rock or sand will be removed.
Certain inverts can handle nitrates fairly well, like certain types of crabs. Unfortunately shrimp don't happen to be one of them. 5 ppm isn't a terrible amount, but it's on the upper end of what most inverts can handle before stress sets in. Fish will show no signs at that amount as long as the water is otherwise clean.
Clayton