I've played through a handful of DOS-era RPGs, and the Adventurer's Journal used in some (all?) of the Gold Box games always stood out to me, where the game would refer you to a specific entry rather than having the story told in-game.

(1) Did other non-gold box games have something similar?

(2) Was the reason for these purely technical (such writers wanting to include art or large amounts of text that would have been difficult in-game) , or was there use an intentional design decision.

(3) What was the last game to do something like this? Have any modern games done something similar?

I can't answer #3, but I can answer 1 and 2.

1: Wasteland and Dragon Wars both had something similar.

2: The reason was partly technical (limited space on floppy disks), and partially a form of copy protection (as it's easier to copy the game disk than to copy the manual).

Interestingly, the developers of Wasteland decided to have some fun with that: If you look through the paragraphs, there are some fake paragraphs in order to throw off those who are reading them. For example:
* Paragraph 1 is a warning about there being fake paragraphs.
* At certain points in the game, you need a password or code in order to continue (like the solution to a combination lock, for example). Sometimes, the paragraphs will have a fake code; using that code may allow you to pass, but will also have some other non-obvious effect that may be undesirable, like making your party sick.
* There is an entire fake subplot contained in the paragraphs.

Dragon Wars has fake paragraphs as well, but they're not quite as good as the ones for Wasteland.

(Do any of the Gold Box games' manuals have fake journal entries? Are any of them good?)

All of them have several fake entries, the information is usually the opposite of what really happens.

The guides tell you which entries are fake.

Simply knowing that there were fake ones in there deterred me from reading entries that hadn't been referenced in game yet.

I've been hoping the come across an adventurer's journal that's better integrated into the game than just a glorified manual and copy protection. Not really sure what that would look like--maybe a murder-mystery where the journal belonged to a dead guy.

There are a number of descent entries thought that have things like pictures, maps sketched on a wall, etc. That kind of stuff is fun. The entries that just recount dialog a lame though.

Most of the old Infocom games did exactly what you want. The games shipped with a bunch of "feelies" like stickers and fake advertisements. They were part of the copy protection as they were also clues for the game. There was information on them to use in the game that was not presented in the game, only referenced, often indirectly.

On the subject of the pictures and especially the maps, that was not only a hardware limitation since graphic files take up a lot more space than text, but also made the journal more convenient for using those maps. Instead of having to copy them down onto graph paper by hand (although I did a lot of that as well), you had it handy in the journal.
Back in the days when these games were made, you could not just switch to another program like Notepad on your computer. You could only run one program at a time. This was true for MS-DOS, the Apple II (which the Gold Box games used a simple custom OS called "RDOS" made by SSI), and the Commodore. Only the Macintosh allowed this, and only if you turned on the Multifinder (it was not permanently on until System 7), which used a lot of memory for late '80s or start of the '90s Macs (got better with the Macintosh II and LC in 1991).
Also as I said, memory was a big issue, especially in the Apple II and Commodore versions which only had 128K and 64K to work with, and the A2 only had a practical 64K. The diskettes on the Apple II only held 140K per side, and unlike the PC could only use one side at a time (so you could get 280K of data per disk but you had to flip it like a record, while the PC somehow got 180K out of the disks but their drives were built to use both sides at once yielding 360K). 140 kilobytes is not that much. Troll GameFAQs and look at the size of many of the FAQs to get an idea since they (until recently) were all plain text files. Any FAQs made before 2-3 years ago are in text.

I am reminded of the NES game StarTropics, which came packaged with a letter. It just so happens that there is a point in the game where you need to provide a 3 digit number, one that you would discover by dipping the letter in water, in order to continue. Frustratingly, this point in the game is well away from a save point, so if you get stuck here, you may have to repeat a sizable chunk of the game if you couldn't answer the question. (You were given infinite tries, but there are 1000 possible combinations (of which only one is correct), and while the game saves whenever you enter or complete a dungeon, there are no dungeons in that chapter.)

Edit: Corrected the name of the game (was Earthbound in the original post, but that's an SNES game that doesn't pull this on you).

While the idea is neat, it does have a couple of flaws.

First of all since the code is static, you could just write it down and pass it on with any copies. Second, if the letter is missing (thrown out becuase it was thought unimportant) you can't complete the game. Third, requiring the paper to get wet before revealing the code has the potential to permanently destroy the paper, ruining future runs if you don't write down the code first.

Yes, it does indeed have those flaws, not to mention the one I mentioned in the post (no saves near that part, so if you have to turn off the game, you have to replay the entire chapter from the start).

This also, of course, presents a problem for re-releases of StarTropics, both on the Wii Virtual Console and on the Mini NES; one can't quite get the same effect here.

(Yes, I did mean StarTropics, not Earthbound; Oops!)

That was a common problem with the "feelie" copy protection of the '80s and '90s.
Especially if it used what appeared to be junk like many Infocom games.
Sierra did that with Manhunter, there was some junk in the box that gave important clues for the game.
A lot of people would toss the manuals and other stuff that came with a game as soon as they go it.
Heck, a lot of people toss the slips with their CD-keys for things like Microsoft Office once they install it. Then their hard drive crashes and when I replace it they hand me the Office CD sans key and expect me to reinstall Office.
"Can't you just call Microsoft?"
No, they'll assume it is pirated and charge you for a new key.
I know it is all DLC now, but I was the go-to person for computer repair in my family and it caused me a lot of grief because people would toss everything but the CD including the keys.

I would assume if you played those games, you were a computer freak, who knew about the importance of those items and kept them.

It's not the same as a person, who only used his PC for work and treated it like a tool, without having any deeper connection to it.