You should be developing the website using the principles of progressive enhancement.
That is, make it work (and look OK) without CSS and Javascript. Add CSS, then Javascript progressively. The idea is that you can use CSS and Javascript to change the original markup and make it work in a better way, but the site will still work well if they are not present. It is the flip side of graceful degradation.
That takes care of accessibility, in terms of general javascript use, and also works well for SEO as your website content will be available to the different bots, whether they use javascript or not.