That said, there are some really annoying bugs in the shake UI (Like the “Show images only” setting that remains when you try to open/save scripts, even though there is no way to change that setting from inside the open/save script dialog..)

To someone actually using Shake, it’s way way more important the interface ‘works’, rather than complies to the HIG, or fits in with the rest of the Apple products.

Of course your looking at the software from a purely visual point of view, but for the higher-end applications, functionality comes a long way before aesthetics. Take any high-end visual-effects/3D application as an example, like Houdini, Maya, Flame etc.

As for the dark interfaces, ignoring the fact colours other than neutral-grey will alter the perception of colour (bad for colour-correction and such - although I imagine it will only be an issue if your interface happens to be bright pink or something) - A lot of compositing happens in dark rooms… A brighter interfaces means more light coming out your monitor, and when you’re looking at that screen for long hours, in the dark - it’s going to hurt your eyes.

I work in the film industry and the 50 percent grey to black look of interfaces is pretty much everywhere. Neutral value in the interface as to not have colour bleed when colour correcting.

Of course now it doesn’t really have much of an impact since usually there’s more light bleeding from the workspace (or from the half of dozen monitors sitting around). Still, an interface that doesn’t grab attention is essential here.

It’s a convention in higher-end video apps, from shake to toxic to combustion. The next update of Nuke is shifting it’s interface to a darker feel. CS3 did the same thing, makes it look like they are playing in the same sandbox.
more of a fad, if you ask me.