I discovered a couple tools that do NOT reencode the sound file, and work on both MP3 and AAC files. So I got to work whacking the hidden tracks. Sorting (in iTunes/Music) by duration found likely candidates pretty quickly.
As always, work on a copy of your original file.
The first is called Audio Splitter. I chose this one first because it said that it preserved the ID3 tags as well, so I'd have less cleanup to do after the splits. Unfortunately, it is a very primitive program. Last updated in 2011, it gives three options for splitting: number of seconds from the beginning, number of files to split to (perhaps useful if you had an audiobook containing chapters of the same duration?), and chunk from the middle (with start and end again specified in seconds from the beginning). I had no use for option 2, and option 3 never worked for me.
The second is mp3TrueEdit. Because of the name I didn't check this out right away, but it does on AAC files as well. It has a free 15-day evaluation during which all features work. It uses the Qt widget kit to be cross-platform, which is workable, but definitely doesn't look native. (The UI looks designed for kids with inflatable plastic and gumdrops.) Anyway, this is more what you expect of a sound editor, with waveform display, etc. It is easy (in most cases) to identify the split points in your copy (another reminder!), and then export the new files. Give them reasonable names in the Finder and throw away the "empty" tracks.
Then go to the file location where iTunes/Music keeps your files. Delete the original file here, so that the app's index still has record of it, and then dump your Trash because the index is smart enough to follow it there. Put your trimmed version in this folder. Try to play the song from the program (do not double-click the trimmed file!)—it will say it can't be found, and ask you to locate it. You select the new file. Ta-da, the duration is updated, and most if not all of the metadata is still there. At this point you can import the secret track(s) as well, and add the metadata if necessary.
For the last step, I find the copy of "NN Some Title" I worked from (which hadn't been damaged in any of my experiments thus far), rename it "NN Some Title orig", and move that to the original location. I don't import it, because I don't want iTunes/Music to index it, but it's there in case I ever need it, without having to re-rip from CD.