I think it also depends on what kind of site you are developing. Whether it’s a web 2.0 application, an online shop, a marketing tool, an informational site, etc…
The people that have JS turned off are such a small minority most people overlook it. On top of that, the majority of people with it turned off assume they will come across bugs in websites (you generally won’t find non-tech savvy people with it turned off, as they wouldn’t really know how).
If there are functions on the site that require JS, you can always include a simple reminder letting people know that JS is required for the site to function properly.
W3 puts the number of users with JS turned off around 5%, and that’s amongst people that actually go to the W3 website. Realistically, that number will be even lower.
This is also where the idea of "progressive enhancement" comes in. Basically you design your site/app/sandwich without js to the best of your ability and then add in the bells and whistles of js – we also do this with css, it’s where the idea of semantic html comes in – what if people have css turned off or using a text-only browser?