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In some of the journals in the library on Myst, I learned that some people lived on the island with the broken ship. Later,
I found Atrus living in a cave.
How did people live in such a place? There seems to be no land for farms. What did they eat? Is this explained anywhere in the series or related materials?
Well as far as Atrus is concerned, while in the game you could only explore that one room, Atrus was actually only trapped on D'ni, (AKA Earth) furthermore, it wasn't that he was trapped on D'ni, but it was that he had no linking book to get back to Myst. It's likely that he could have gone to any other age he wanted. Even if he couldn't I'm sure he had plenty of supplies, as he was stuck there for over 30 years.
While living on Myst, Atrus and Catherine spend quite a bit of time in both Riven and D'ni. And as seen in the library on the island, quite the collection of other linking books, and most likely got everything they needed from those other ages.
Channelwood, as described in the journal, used to be a very populated place, however a global calamity caused massive flooding and killed off most of the humans that lived there, leaving only a few of the Ape-like creatures that lived in the tree huts above the surface. Likely they foraged on critters of fished before Atrus's sons killed or drove them all off.
The "real" Myst Island is substantially larger than the island depicted in the game. Both Cyan and Myst (the game) exist in the Myst universe (in much the same way as Marvel exists in the Marvel universe). In-universe, Cyan simplified Myst Island to make the game both easier to develop and easier to play.
According to Richard Watson, writing from an in-universe perspective:
I want to start by pointing out that Myst/Riven are Cyan's attempt at recreating some of the events in the life of Atrus in a semi-non-linear medium (i.e. a game). Since it's a game where the player can do things that didn't happen in the account of Atrus' life, we've got to take some artistic license with his story - like the "losing" endings of Myst and Riven.
When making the games, we have to carefully pare everything down to the basic elements needed to play the game, leaving out almost anything that isn't required for gameplay. Myst Island, for example was made much smaller, and only the buildings/places relevant to playing Myst were included. Atrus definitely had other "places of protection" for his Books other than the ones shown in Myst. We throw in as many "extras" as we have time for, but for the most part, there isn't much time for things that aren't specifically needed for a playable game.
So the most accurate answer for many of these kinds of issues (e.g. "Why do the remaining Books coincidentally happen to be the Books with 'places of protection'?) is simply "artistic license". If we didn't have hardware limitations, storage capacity limitations, time limitations, money limitations, etc. and if we had a billion monkies [sic] working on a billion computers for a billion years, we could make the Ages more complete, which would be cool from an exploration point of view, but wouldn't make the games themselves any more playable. In fact with all the "non-game related" things thrown in, there would be a lot more "red herrings" and people would be even more confused when they write to me. ☺ (If I had a nickel for everyone who wrote to me asking what one of the few "extra" items in Myst did...)
Watson does not specifically mention farming or other food sources on Myst Island itself, but we can extrapolate the presence of such things, as well as living quarters for Atrus and his family and so on. If these things were not on Myst itself, they must have been on other ages, but either way, they were "deliberately" cut from the game for reasons of scope.
