I don't have the N900 and its charger (yet). But the description sounds like could be caused by two possibilities:

1) The switchmode charger, when load gets lighter, does reduce its switching frequency. At some point is becomes so low that it falls to audible band. One reason to reduce frequency is to improve efficiency with lighter loads (likely to meet some Energy Star requirement...)

2) The N900, when getting to almost full battery, changes its internal charger behavior so that it starts to take charge current in bursts. (Kinda like trickle charging). The bursts frequency may be low enough to be in audible range. The bursting current causes a change in charger output filter inductors, which cause a change in its core magnetic flux. This change in flux tend to cause force that changes the inductor core shape slightly, and will be transmitted to air. (It is like piezoelectric effect.)

In either case, this is not a malfunction or defect, and there is not much you can do to help this.

Does everyone who has the N900 and factory supplied charger have this issue?

EDIT: Got my own N900 and noticed the same issue. However, I do use my old AC-4U charger with the USB adapter. Therefore I can confirm it is not an issue with AC10 charger, but N900 itself. Therefore the option 2) appear most likely correct answer...