This is a good question, since it is obvious that the word, at least today, could be read in one of the two opposite ways you mentioned. This description of a "cobblestone slum" near the valley of ashes in The Great Gatsby by F. Scott Fitzgerald is replete with imagery of poverty and hopelessness. Because of that, an interpretation of "undeserted saloons" which says no one is in them because there is no money to spare is as sensible as an interpretation of "undeserted saloons" which says that everyone is in them because their lives are so depressing that they have to drink. To make matters worse, "undeserted" can mean either fully inhabited or abandoned.
So, I looked to an outside source for an understanding of the usage of "undeserted" during the 1920s, and this is what I found for you. One source, linked below, says this:
“Saloons of the faded-gilt 1900’s” were bars that would serve alcohol to those without any money. That’s why they were never deserted. It was things like this that led to the Great Depression.
In the book Lost City: Fitzgerald's New York, also linked below, the author suggests that this "cobblestone slum" is one of Fitzgerald's many nameless places associated with poverty. In this particular place, there is obviously a well traveled road (which is how Nick sees it as he rides past it in Gatsby's car), yet there is no real sign of life anywhere.
[D]espite the lure of Prohibition's forbidden fruit, the area is still an undesirable one.
The author's point in her book is that, despite the fact that everyone is visiting this string of dark saloons for their free alcohol, the area is still barren and unproductive because there is no money with which to make things grow and prosper.
Given these two resources, it seems that the correct reading of "undeserted" in this passage from The Great Gatsby is "full of people." Thank you for prompting to learn something new.