No, this shouldn't have changed. In Worklight 6.1 (and 6.1.0.1) the servlet schema version in the web.xml should be 2.4. There was an issue in Worklight 6.0.0.0 and 6.0.0.1 where the schema version was set to 3.0. But once that issue was identified it was fixed via APAR PI05761 in Worklight 6.0.0.2. So, in Worklight versions 6.0.0.2 and later and 6.1.0.0 and later, the servlet schema version should be set to 2.4.
I just created a new project using the 6.1.0.1 studio and my web.xml has this:
<web-app xmlns="http://java.sun.com/xml/ns/j2ee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
id="WebApp_ID" version="2.4"
xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd">