Unmaintained applications may come with bugs and security vulnerability and can be a threat to the security and integrity of the web server.
Since different applications on the same server are likely to share the same security context, an attacker may leverage vulnerabilities in one application to gain a privileged access to an adjacent application, which would have been otherwise secure.
Two applications can coexist if they do not share the same security context. This can be achieved by enforcing a sandbox mechanism, like chroot for example, and by not letting them interact with the same resources, i.e. the same database.