As explained here, a large part of Sweet Home 3D Java is transpiled to JavaScript, but some classes too complicated to transpile as well as all the code which handles the user interface were rewritten in JavaScript (see src folder in SweetHome3DJS project).
Therefore, as the transpiled part of Sweet Home 3D JS is generated from Sweet Home 3D Java code, SweetHome3DJS project depends on SweetHome3D project, and keeping this dependency helps to benefit of bugs fixes programmed in SweetHome3D project by just transpiling again the classes needed in SweetHome3DJS project.