I prefer to use the package.jdo XML metadata rather than annotations, but you don't seem to have specific documentation for this.
Your documentation for JDO annotation @Index mentions that it corresponds to the XML <index> element which is one way to specify indexes in XML metadata.
But there is another way which is to specify an indexed attribute on the field element, like <field name="foo" indexed="unique"...> or indexed="true". It doesn't seem to be mentioned on the JDO annotations for fields documentation. Could you confirm whether objectdb supports this?