On all the projects I’ve worked on, I always try to follow the MVC arquitectural pattern, separating the model from the view *and* creating a controller. It may be a simple controller in charge of a tab-set, or an accordion. Or it may be a full size controller in charge of the whole page structure, on sites that make an extensive use of javascript.
Either way, I always have a controller for a dynamic section of the page and the controller always works with the container of that section. If I need to reference any element inside the container I will use this.container.getElementById() or this.container.getElements(), which will do a search only on the child elements of the container and not on the whole dom tree of the page.
Yes, it is very usual to see nowadays code that alters the links of a page 
