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...

All my nokia chargers, from old 3.5mm to n900 whine.
I haven't heard n900 speakers make noises when gsm radio is active though, my older nokia phones all do that.
My N800 makes an extra higher pitched noise over the already high noise floor when the touchscreen is touched. The backlight seems to vary in brightness at lowest setting depending on sdio activity...

When you open your ears and eyes you'll discover that everything makes noises or flickers these days

Whine:
That's because save from UPSs and high-power devices all chargers, adapters, etc make use of SMPSUs (the small and light chargers, as opposed to the old wall units that would break a window).

Flicker:
In Europe at least, all incandescent lighting is all but banned (In Romania it's about to get illegal to sell I hear), thus everyone moving to gas discharge lights. Minus the CFs that have SMPSUs inside (those whine), they all flash rapidly as the ballast pushes electrons in the gas (so to speak). 60Hz US, 50 everywhere else.

In addition to this, all backlights in panels, TFTs, etc use CF technology which is exactly like the flicker kind except they flicker faster and at higher voltage (making them flicker-"free" and efficient). However, as the gas oozes out with time, gets contaminated by the electrodes, etc, generally age they start to lose their effectiveness and only fully light every few cycles, effectively reducing the flicker from 100-600Hz for CF/TFT to around 50-60, making them slightly flicker.

In addition to that, most "on" and "standby" LEDs are wired into the power supply to see when it's dead, usually via a gas discharge small lamp (orange) or LED with a resistor and a diode. As a result, they are powered directly at mains frequency, thus, flicker. Orange find-in-the-dark light switches are easiest to see.

Add this to the fact that public illumination use 50/60 HZ had discharge (sodium lamps), and you see why it's true.

Yes, the whole world whines and flickers. Welcome to the 2000s.

20 years ago, it was all yellowish from the low-powered bulbs and it hummed at mains frequency. Those a little older know what I mean by this: TV hummed, fridge hummed, the stereo and radio hummed.

In fact, mains is in sync in the whole area so if you had very fine ears, the whole world would hum as the city concrete slightly moved the heartbeat of technology.

I have always been super sensitive to noises.

My laptop PSU is too annoying to leave charging overnight. As others have said, its fine while charging but once finished its too loud.

I haven't noticed anything with my N900 though, although I wont leave that on overnight anyway as I will be using it to listen to music in bed last thing at night.

I used to love taking walks in the middle of the night in the sleeping city and listen to the "beat"

The n900 is generating a lot of EM when charging - further to my comment upthread about not being able to use an aux cable while charging, I can use it just fine when not charging. While charging, there;s a horrendous squeal comes over the speakers as the n900 it too 'hot' to be connected. Which is a bit of a bummer on long trips when you don't want to burn battery.