There are about 7 or 8 Great Harbour owners that opted to have us add our factory sea chest to their older boats. Ask ANY one of them about it and they will tell you it is the best upgrade they have ever done to their boat. The top of the sea chest does indeed extend well above the waterline, so you can remove the lid (with thumbscrews on a Great Harbour sea chest) and get in there to clean the hull screen (most owners keep an electric pressure washer in their engine rooms to blast away growth once a month or so). You can also install another seacock without hauling the boat and without pumping the sea chest dry. We've done it several times. If you're careful, you get less than a quart of water in the bilge while doing it. As was pointed out earlier, it is also pretty convenient to have all of your seacocks in one place.
The biggest advantage though is that you eliminate the need for sea strainers - and the extremely un-fun job of cleaning them! A typical seacock on a mid-size trawler is going to have an opening of about 3/4". Do the pi-r-squared math and you come up with a little less than a half square inch of surface area. Figure maybe five seacocks on a typical modern boat and you have ALL of the saltwater entering the boat through less than 2.5 square inches. That's a lot of flow - and explains why jellyfish, weeds, sand, plastic bags, etc., all get drawn into our sea strainers.
On a Great Harbour, the hull grate measures 8 inches square and is covered by an approximately 60% screen. So, do the math again - 8 times 8 times .6 equals 38.4 square inches of surface area - you're drawing the same amount of water through SIXTEEN times the area. Consequently there is almost NO suction that can be felt at the hull screen. It doesn't pick up any of the aforementioned nastiness - and a plastic bag won't get sucked up against it. In fact, the main reason to have a hull screen at all is to keep fish from swimming into the sea chest!
Before we had sea chests on the charter boats in the Bahamas, I (or whoever was on duty) had to change three or four generator impellers per season since our charterers often decided to test our shallow draft claims by anchoring overnight in three feet of water! However, after adding sea chests, the only time we ever changed impellers was at the beginning of the season.
Done properly, and with some thought to hose routing, a sea chest isn't the cheapest way to get raw water to the various engines/generators/airconditioners/watermakers/heads that need it, but it is, in my opinion, the best way.