Welcome Matthias. Thanks for trying this port. [:)]
From your post, it seems you just have to use FreeBSD Java 3D DLLs, right?
If you want a portable Jar executable file able to run under Linux and FreeBSD, you could add the FreeBSD DLLs in some freebsd/i386 and freebsd/x64 subdirectories of the archive and test the operating system in SweetHome3DBootstrap.java to select the right directory with System.getProperty("os.name") which should start with "freebsd" in lower case.

By the way, note that I should use Java 3D 1.6 in future releases of Sweet Home 3D, based on JOGL. Do you know if there's a port of the latest versions of JOGL under FreeBSD or if it's difficult to achieve?