Disadvantages
While the water the spacecraft landed on would cushion it to a degree, the impact could still be quite violent for the astronauts.
There are several disadvantages for splashdowns, foremost among them being the danger of the spacecraft flooding and sinking. This happened to Gus Grissom when the hatch of his Mercury-Redstone 4 capsule malfunctioned and blew prematurely. The capsule sank and Grissom nearly drowned.
Another problem associated with splashdown is that if the capsule comes down far from any recovery forces the crew are exposed to greater danger. As an example, Scott Carpenter in Mercury 7 overshot the assigned landing zone by 400 km. These recovery operation mishaps can be mitigated by placing several vessels on standby in several different locations, but this is quite an expensive option.
Read more about this topic: Splashdown (spacecraft Landing)