Yes; as I wrote, Thief takes well to episodic fan missions. The formula works. A few reasons:
It is easy to find a motivation for action. It can be as simple as "I have a simple job planned for this evening. Break into a guarded mansion, steal another fat nobleman's priceless trinket, and leave quietly." If you want more than that, most Thief stories follow film noir patterns, which mesh very well with the gameplay.
The games also give you a strong set of baseline assumptions, which work in your favour. You don't have to start from the beginning and build a whole world. Add Hammerites, and players will know what they are dealing with.
On the other hand, the city is expansive, and can accommodate several different stories. It has no solid, well-defined limits.
You can deliver a self-contained mission/story within one level, which can be any size you want. You don't have to do a whole campaign, and you can scale a project to your abilities/free time.
There is no character advancement. Garrett is always Garrett, with the same general capabilities except equipment, which you can easily regulate.
Most AI attack you, flee from you or disregard you. You don't have to develop complicated interactions, or do voice acting (which tends to be an "expensive" development resource for fan projects). You can communicate most of the story through readables and environmental clues. (Actually, it seems to me a lot of Thief authors and players want story first, aesthetics second and gameplay third. There are much fewer purely gameplay-oriented levels than levels which tell some kind of story. This also means you don't have to be a technological wizard to make a mission.)
Both the Dark Engine and idTech4 are newbie-friendly, with relatively low barriers of entry and shallow learning curves. Many modern engines use custom-built models for architecture, which you have to create in an outside app, and import into the actual game editor. This can go wrong at three different points, and requires expertise in four fields (modelling, texturing, conversion and level building) instead of one.
As a side note, it would be relatively easy to imagine a different Thief, one that had a text-based conversation/trading system like Ultima Underworld,
and I am sure a lot of authors would prefer it to what we have. However, the game's focused nature and specific limitations also make it less likely for someone to get carried away and make something over-ambitious. It still happens all the time, but there are some hard restrictions.
In comparison, System Shock and Deus Ex are much more specific, and require you to put a lot more work into the story, levels, interaction possibilities, character stats, and more.
But I think it is mainly about that specific combination of strong focus and high variability that makes Thief well-suited for fan missions. It doesn't hurt that there is an established community playing, commenting on, and building fan missions, but that's more about momentum (which seems to be stalling, unfortunately), not the initial reasons for popularity. This community is also special in that it has a lot of people who aren't typical gamers. They often tend to be older, there are more women, and far less techies than in the regular FPS scene. Maybe that's also something which matters.