Its actually quite a dangerous way to create your ids, for there is no guarantee that dnn_ctr will always be the naming container id.  What I usually do is assign a variable the namespace from the module. 

var m_MyModuleNamespaceVar = '<%=MyControl.NamingContainer.ClientID%>';

then in my separate js file

var ctl = $(m_MyModuleNamespaceVar + 'mycontrolname');

You could put in in the page_load event of the codebehind.  However, it is probably much easier to include it in the ascx file.

just make a script section with the following

< script language=........>

   var m_sMyNS = '<%=MyControl.NamingContainer.ClientID%>';