It appears the Notepad++ developers agree with you and may be about to change how this works. See HERE and you may want to add your vote endorsing it there.

EDIT: Well, the developers actually linked here, so I guess they already know your opinion. :-)

For example, instead of spending 3 minutes to do the same edits that I usually do, I spend 4-5 because I always have to confirm on the popup. And again, this happens almost every day.

There are 2 different buttons, clearly labelled. If some users are incapable of choosing the right button, then I should not suffer the consequences. Even so, if someone replaces something across multiple files by mistake, what is the problem? They can close the files without saving and reopening them again. Very easy.

I simply do not see this new popup as a feature for a daily user of Notepad++. At least there should be an option to disable it!

You are right (IMO). Why is one little extra Enter press such a problem?

Sometimes I think people are intolerant to any sort of change, even when it exists to protect their data (which is what I believe this confirmation was introduced to do).

If Notepad++ developers can’t change their product (for the good) without having for every single aspect some setting that restores old behavior (e.g. this one, backward regex searching, probably some others), then, well, I think that is too bad.

We cannot edit the codebase in the Forum. The Forum has a FAQ at https://community.notepad-plus-plus.org/topic/15741/faq-desk-feature-request-or-bug-report which explains the proper place to make a feature request. I highly recommend fully reading the FAQ before submitting the request, and making sure you are asking politely (your last statement in the Forum sounded more like a demand than a polite request – I cannot know whether you intended it that way or not).

However, is it really that onerous to do one extra click or keystroke during a replace-all-in-all-open-docs? If it is that awful for you, then while waiting to see if your request is implemented, you might want to downgrade to a slightly earlier version, and turn off auto-updates, so that it will go back to old behavior.

It’s a safety feature, to protect your data from an accidental click in the wrong place (some users complained about not having this safety net.
It isn’t turn-offable.