Beamer (and from the same author TikZ/PGF) follows the compartmentalization scheme. What you are describing is still following that scheme actually but in a larger scale.
It is both a class and it has its internal packages (themes actually).
- Why is it a document class ?
Because, it alters the page size, page elements, typical title and author placement mechanism, figures and captions etc. Hence you cannot use it together with other classes. It fundamentally replaces many common LaTeX mechanisms. enumitem package is an unfortunate loss for example in beamer as usually they don't play nice together. Thus, it is necessarily a document class.
- Why are there so many
.sty files?
That's because of the bottom/up design, every page has internally comprise of a few choices, in beamer lingo; templates. You can select different templates for different components, say, I need a split footer and a header with section dots and also that color scheme. This is possible since every sub component is a pseudo-package that you can combine and call it inside an encapsulating theme with \usetheme{foo}. Then it will go and grab the necessary contents from those .sty files. But I can make another theme {foo2} and change only the colors and it would be a matter of a one-liner. Had it been as you have quoted. It would be a huge mess. Notice for example that if you only need a for loop. You only need to say \usepackage{pgffor} instead of loading the whole TikZ suite.
I think that manual is rather a guideline instead of a PEP8 type of forcing. So you don't need to setup a religious view around it. And the authors know exactly how difficult to keep track of package conflicts hence it is a conservative approach.
