The more modules you have enabled in your web server, the more complex the code and interaction between these modules will be. The more complex the code in your web server, the more chances for bugs there are. The more chances for bugs, the more chance there is that some of those bugs may involve security holes.
Before you put the server into production, review the server setup and disable any unused modules. As time goes by, the server enviroment may change and some modules may not be used anymore. Do periodical revisions of your setups and disable modules that aren't in use.