JEuclid uses an identity transform to save the SVG file. When Saxon 6.5.5 is in the CLASSPATH, this identity transform is implemented by Saxon 6.5.5 and not by the XSLT processor included in the Java runtime. The identity transform implemented by Saxon 6.5.5 does not seem to be namespace aware (hard to understand why). Hence the namespace declaration missing in the SVG files generated by JEuclid.
* I had to patch JEuclid to workaround this problem. You can download patched jeuclid-core.jar from this private download area: