It depends what you do with jQuery. Maybe you use a nice , well tested and full featured plugin (calendar, grid view) then jQuery works. Or if you want to manipulate html (you grab an html from a page and you want to export it as epub but you want to remove some stuff before, cleanup some styles, jQuery is much better at DOM manipulation then pure JS)
IMO what you should never do is put your application state inside the DOM if you have a complex page/app.
Shopify is a great example. They have both, but in the right places. The websites themselves are not SPAs, because they don't need to be. A minicart is barely reason to pull in an SPA framework and architecture, so they didn't. But their live theme editor tooling makes full use of the power of an SPA.
IMO what you should never do is put your application state inside the DOM if you have a complex page/app.