I think there's something poetic about crumbling buildings. Maybe I'm reading too much into it, but as an architect, there's something about being a creator that allows you to see a physical representation of what you had in your head, some sketches on paper, suddenly in real life, towering over you.
It's kind of like being a writer - of novels or screenplays. To see something you had in your mind, or on paper, suddenly become a real thing (a book, or a movie), would make you feel like a god, almost.
If Nolan has a phobia (which I don't think he does), I'd say it's quite simple: Seeing something you created, deconstruct. And there's something terrifying about how easy it is to destroy something that took a long time to build.
- It's easier to blow up a hospital, than it is to build one.
- It's easier to burn a book, than it is to read one.
- It's easier to kill someone, than it is to build a relationship with them.
Overall, destroying is EASIER than creating, almost all the time.
To take it one step further, it almost shows how ass-backwards the League of Shadows is when watching BB.
- Ra's wants to destroy Gotham in order to re-build it.
- Bruce actually wants to re-build Gotham by helping and creating symbolism, not by destroying.
All of this stuff ties into Inception, too. Cobb and Mal, the idea of creating worlds, and so on and so on.
I'd say a very central theme of Nolan's films is the balance between creating and destroying:
- Memento: Destroying memories, creating new ones / false ones.
- The Prestige: Creating copies of yourself, destroying them.