One more update: by storing the initial focus state, moving the focus incrementally by small amounts (10 units in my current app), and slowly returning the focus to the initial state in the app's destructor (in my case, stepwise by 10 units every 50 milliseconds), I have been able to eliminate the clicking noise.

I don't know how important it may be to control the focus in this way (as obviously any N900s that might have been damaged by this would probably already have been by now), but I think it might be a good idea for other app writers to be wary of the N900's focussing mechanism...