I've had three N900s and all three have developed spots over time. It could certainly be coincidental, but it seems (on my devices anyway) that the spots developed after situations were my n900s were allowed to run hot for long durations.

Since I had a spare still under warranty, I had the LCD replaced just for the hell of it. We'll see what happens, but I'm guessing that the spots will come back eventually. In the grand scheme of things, it's not such a big deal. Unless I've been terribly unlucky, this seems to affect most if not all N900s, so there's no sense worrying about attaining the unattainable "blemish-free" device)...