My observation will come from the point where ajax is still on and you don't want to put your javascript/css inside a page BODY.
When ajax is on only first page is loaded into the DOM, in every other page only BODY will be loaded (no point in having several HEAD's inside a DOM).
Because of this your javascript must be placed inside a first HTML. Now it doesn't matter if you want to use 1 js file or several of them, as long as they are initialized inside a first HTML.
I have another article dedicated to this so take a look: Why I have to put all the script to index.html in jQuery Mobile
I will only show you link to my other answer regarding this topic, there you will find several solutions with examples, search for a chapter "Data/Parameters manipulation between page transitions" : jQuery Mobile: document ready vs page events
Everything I said for javascript also reflects here. It doesn't matter how much css files you use as long as they are initialized inside first HTML file.
EDIT :
I am always ready for a healthy discussion. ;)