When aircraft enter the water, they explode, killing anybody in or near in. There's really no reason for a helicopter to explode underwater, especially since the water would put out any fire or sparks anyway.
Aircraft should instead become immediately inoperable and suffer critical engine damage, just like cars. Additionally, helicopters shouldn't take engine damage until the actual engine is in the water, currently even the skids case engine damage when wet. In Arma 2, players could dunk half the helo in water, and as long as no instruments or rotors got wet, you could tug it out of the water.