In this case every call to the DOM goes from a slow baby crawl to rocket speed. In no other aspect of life do people make such empty excuses, using cliches no less, to intentionally remain in the stone age.
Totally depends on the situation.
And why the assumption that modern versions of jQuery don't make use of modern DOM APIs?
* querySelectors (standard or the home grown Sizzle engine)
* Method chaining for trivial tasks, in many cases to compute data that is already statically present or directly assignable.
Regardless of whether jQuery is using modern APIs or not there are old standards available, to JavaScript, that just about everything in jQuery eventually compiles down to. At the end of the day it becomes a matter of whether writing a couple of 3 line abstractions is far too hard of work or whether it is simply easier to push everything through 65k of jQuery purely for the sake of familiarity.
I've worked with developers who completely ignored good libraries and instead created their own terrible implementations. They got nothing done and what they did was a buggy mess that often needed months of patching.
Finding a good middle ground is the best way to go and when the loading time increases by only a few milliseconds, but the development is a lot faster and cheaper, that's a good compromise in most cases.