There’s a great article on how diagrams were used to track puzzle dependencies in the Monkey Island games. There’s a related thread on this site here.
On the topic of using UML for puzzle/story design, here’s a work in progress of mine which might interest you as an example. I drew it with Inkscape, hence the SVG.
It wasn’t easy to arrive at. But it’s the best I’ve been able to achieve so far. This particular thing is not an IF-style puzzle, more a non-linear narrative. The reader is able to travel between locations and witness the story unfold, in a Christmas Carol kind of way.