We're actually not necessarily looking to reduce use of these things.
Are you talking about Javascript here or Java? The latter is renowned for being insecure, but modern websites rarely, if ever, rely on Java anymore. It requires your browser to have a plugin installed and enabled.
In terms of Javascript it is possible to introduce some security issues but I wouldn't necessarily go as far as to say it "plagues" modern websites. XSS issues are somewhat common, but they are often difficult to find and exploit. These types of issues are not inherent within Javascript itself, instead they are introduced inadvertently by the developer.
I don't know the specifics but I'm fairly sure neither IPB or VB use Java so maybe there have been some Javascript related bugs here.