There are a few designs which can be modified to sit "in" rather than "on". Most of these are larger boats, such as the Yankee and Skeeter class boats.
But in the smaller range, you have Nite. This can be built from plans with a wooden fuselage, or purchased complete with a fiberglass body. Find the link on the Icester links page. (
http://www.icester.net)
There is a small boat called the "Isabella", which is also linked at icester.net. It is built with common lumber, and an assembly kit. It works with a windsurfer rig, I believe. At one time a cover was offered, or suggested, which would make it semi-enclosed.
Of course the other small boats, such as the DN and the Arrow, and such, are open.
Then there is my Icester design, in which two can ride, and is semi-enclosed for warmth and comfort. Rich.