Most of these utility functions are fairly straightforward and will rarely require any changes or maintenance. Testing should therefore be straightforward as well. Having the whole community back something doesn't mean it's bug-free, and sometimes it makes it harder when their release cycle isn't as frequent as you'd like it to be.

Having said that, it's all about tradeoffs. Whether your project needs something as big as <insert JS framework or lib here> or if you can live with just needing a few utility functions, you make those choices, doesn't mean one is better than the other as it all depends on context and situation.

jQuery has become the defacto must-use library for javascript now which IMO is unfortunate, as a lot of sites and apps include it when they barely use most of what jQuery offers. I'm guessing most use jQuery for only a few things - Ajax, DOM querying, and events. I hope that sometime in the future jQuery would be more modular.

If you search for classList on npm you get a half dozen results. I disagree with your assessment here.