Maybe I can offer a bit of perspective as somebody who doesn't even do React stuff yet!
I think back ten years ago JavaScript was a little more 'wild west' than it is now. We have excellent sites like http://caniuse.com which allow us to quickly find which browsers support which features, but ten years ago it was a little different.
When jQuery first came on the scene it let you write cross-browser JavaScript! It was like a CSS reset for the differences across browsers and allowed you to write your code once and have it work everywhere.
Today's JavaScript has been shaped and improved by some of the ideas in jQuery, and so today writing in jQuery doesn't offer quite the same benefit as it used to.
Personally, I worked with and around jQuery code for years and it served as a barrier to understanding. Everything you do you have to do 'the jQuery way' and unless you're somebody who already knows what they want to do, these sorts of shortcuts can be really confusing. On the other hand, once I made it my mission to learn vanilla JavaScript, everything fell into place.
Now whenever I am given a piece of jQuery code I have to first refactor it into vanilla JavaScript to understand it, then I can continue fixing or working with it.
Sometimes my vanilla JavaScript does turn into jQuery after I've finished with it (by other people on the team) but I can't imagine what benefit taking code and making it dependent on an external library offers.
Now here's my guess as to why React folks aren't thrilled about jQuery - React is another library where everything has to be done 'the React way' with things 'inside' React, just how jQuery takes your logic and makes it 'inside' jQuery.
I think the final blow to the jQuery vs React question came when John Resig, of jQuery fame, tweeted that he does most work in React now (as opposed to jQuery) which many saw as the writing on the wall for jQuery.
Hopefully that sheds a little light on why your jQuery code might end up getting converted to vanilla JS, or even Reactified, instead of being left as-is.
My recommendation to you would be to try to learn vanilla JS as much as possible and leave jQuery for when you really need it. By default, try writing vanilla JS first and see how far it gets you :) For me when I stopped trying to work with jQuery is when I finally was able to dig in and learn JS. :D
Here's a great reference I used for learning JavaScript: http://youmightnotneedjquery.com/
And another for unlearning jQuery: https://gomakethings.com/ditching-jquery/