When descaling an HX espresso machine, it's obvious that running a citric solution through the heat exchanger itself is important to prevent a scale build-up there. Some sites state that descaling the boiler is even more important. Why is that? The scale will of course build up at the water line, but will that do any harm to the machine?

The boiler, where the steam is produced, is more likely to have a heavy build up of scale. This can cause things like a decrease in total volume, heating element failure, over-pressure from a clogged pressurestat, and over-filling due to a scaled water-level probe. Other than that I wouldn't worry about it..

Scale is most likely to build up heaviest where the water is hottest: On the heating element. When the water boils it leaves whatever is dissolved in the water on the heating element. Sediment build up reduces heater efficiency and can raise heater internal temperature.

Based on Jim Schulman's "Insanely Long Water FAQ", I decided against descaling the boiler, and instead will do weekly refilling of the boiler with distilled water (spiked with a small amount of regular water so the autofill switch will turn on). My reasoning:

1. Descaling the boiler seems like a pain in the butt.
2. Since my machine runs hot and requires long cooling flushes, I didn't want to use RO or Crystal Geiser water all the time due to the expense and potential effect on taste.
3. Since I don't use the hot water wand normally, filling the boiler weekly with distilled water should keep my boiler free of scale.

This combined with monthly or bi-monthly citric acid flushes of the HX seemed like the simplest descale routine for me.