Okay! That was quite a bit of research, but I seem to have figured out what happened in 6.4, though I'm speculating with limited information in some places:

At some point prior to JJ2+ v4.0, which is the earliest that we have records of, BlurredD added some code to detect server queries, e.g. from GIP scripts. The code was intended to look at TCP packet 0x0E and run if either of the following two conditions was true:

• The numberOfPlayers byte equaled 0, OR
• playerName began with the section character followed by the pipe character (|)

If either of those conditions was true, the code was meant to write the Server Query line to iplog001.txt (or whatever), send the client any useful information, and then kick the client.

I can see that both DJazz's SGIP script and jj2multiplayer's fork use names beginning in section-pipe, though neither of them sets numberOfPlayers to 0, so JJ2+ has to rely on just the player name. I'm assuming without evidence this has always been the case and the packet sent by SGIP has never changed.

(The SGIP packet is, incidentally, incorrectly formatted... it uses the packet format from JJ2+ v1.3 or earlier, but claims to be JJ2+ version 3.0. However, JJ2+'s code for reading packet 0x0E was also never updated for version 1.4, so JJ2+ was looking at the right byte all along.)

Crucially, at some point somebody accidentally used the wrong character encoding to save the JJ2+ source file that reads packet 0x0E and checks names for section-pipe. This was publicly visible in that, for a while, when players joined LRS servers and were automatically set to zero lives, they saw a green A (with a diacritic) at the start the following two lines, which was an artifact of using the wrong character encoding for that source file:
This was later fixed by saving the file with the correct character encoding. Probably this happened in 6.4.

While the file's character encoding was wrong, instead of comparing player names to section-pipe, they were instead compared to A-section-pipe. That meant that the server query line stopped appearing for a while, although for many years before that, it had been reliably appearing in iplog files as intended.

In summary, 6.4 accidentally fixed an unknown bug that was preventing the server query line from appearing.

According to BlurredD in 2014,
However, according to stijn in 2023,
So that's puzzling! Did something change between 2023 and now that caused SGIP scripts to stop using the query packet and go back to using packet 0x0E? Or was stijn talking about a different SGIP than the djazz.se and jj2multiplayer.com pages?

I'm limited here without knowing how SGIP works, but I'm wondering if maybe SGIP is sending the query packet and packet 0x0E, but not actually using the response from 0x0E? Because if I'm reading the JJ2+ code right, trying to join a v4.0 (or above) server and pretending your client is v3.0 is not actually going to give you any useful information, assuming the server has /latestversiononly enabled, unless the server treats you as a server query.