Do not unload JavaScript and CSS was a deliberate choice, not an accident or oversight.
First of all, understand that page controls are just a JavaScript construct - the browser is unaware of this. The browser just sees a piece of the DOM that is dynamically generated by scripts.
The web platform does not allow you to download script files - as soon as they are loaded into the context, they are there forever.
Using CSS, they might try to remove the tags, but it opens a jar of worms. Depending on which pages of the order are sent, you can use different styles used in one application. What if two pages belong to the same stylesheet? Do you add the same link tags twice? And which one are you deleting?
This is a mess. Instead, WinJS ensures that scripts and stylesheets will be loaded once and only once when they reference them. Thus, you can have each page in the link to the application "myStyles.css", and it will load only once (and there will be only one style tag).
So what do you do to prevent the problems you see? First, remember that you are creating an application, not a website, that will arbitrarily grow new content. Decide your common styles and classes. Put the general style in your default.css and refer to it from the default.html file.
For individual pages, the easiest way is to attach your styles to the page name. Instead:
<div class='intro'></div>
do
<div class='page1-intro'></div>
Then you are guaranteed to avoid collisions.
If you link to page elements by ID, do not do this. Using the identifier on the pages causes all kinds of potential oddities (what if you perform the same page management at the same time? The identifier does not exist until the page is loaded into the DOM, which means that the data, option links by ID do not work) . But if you insist, again, consider the identifier prefix with the page.
Basically, create special namespaces so you don't run into. This is much easier than hacking link tags manually and will lead to a much better experience with applications than doing full navigation.