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Wikipedia states that

The telescope had to be kept in a clean room, powered up and purged with nitrogen, until a launch could be rescheduled.

Spacecraft are always kept in a clean room environment. My question is, why should it be kept purged with nitrogen?

Would keeping it in a vacuum chamber instead of a clean room be a good idea?

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    $\begingroup$ For the record, spacecraft aren't always kept in a cleanroom environment. $\endgroup$
    – PearsonArtPhoto ♦
    Commented Sep 11, 2013 at 13:18

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Nitrogen is a relatively inert diatomic (N2) gas, but also importantly, while there are other gases that refuse to react with much anything even more so, like e.g. Helium, Nitrogen is cheap since it's often a byproduct of industrial processes. It is also frequently readily available at scientific facilities in its liquid form for being an extremely effective coolant that doesn't damage electronic equipment or leave colored stains on optical equipment.

Since it's relatively light (atomic number 7 on the periodic table of elements) it will also expand pretty well in all directions and displace any impurities that might still linger suspended in air. It is also non-toxic, non-corrosive, non-hygroscopic, colorless, odorless, tasteless, and will displace Oxygen (O2) and greatly reduce fire hazard and oxidation.

I.e. it is the industry standard technique for the replacement of a hazardous or undesirable atmosphere with an inert dry atmosphere by displacement or dilution.

In case of the Hubble telescope however, the reason is also described in the same Wikipedia article a bit later on:

A shroud of multi-layer insulation keeps the temperature within the telescope stable, and surrounds a light aluminum shell in which the telescope and instruments sit. Within the shell, a graphite-epoxy frame keeps the working parts of the telescope firmly aligned.

Because graphite composites are hygroscopic, there was a risk that water vapor absorbed by the truss while in Lockheed's clean room would later be expressed in the vacuum of space; the telescope's instruments would be covered in ice. To reduce that risk, a nitrogen gas purge was performed before launching the telescope into space.

This should also answer your last question regarding storing the Hubble Space Telescope in a vacuum chamber instead. While a vacuum chamber could prevent in-air impurities by simply sucking all the atmosphere out of it, that process wouldn't clean it of possible water molecules gathering on and around its hygroscopic multi-layer insulation, if they started condensing. It is also pretty hard to find a vacuum chamber large enough to hold the whole telescope, and a malfunction of its pump could result in a sudden gush of air, damaging the telescope and its shroud.

In contrast to a vacuum chamber, using Nitrogen only results in a slightly changed atmospheric pressure when the clean room environment it was stored in would be accessed by the staff working on it. They also wouldn't need expensive and cumbersome pressure suits, and any Oxygen supplied Hazardous Environment (HEV) suits would do just fine for such tasks.

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    $\begingroup$ In a vacuum, the vapor pressure of water is lowered. Any water left would be in gaseous form (and eventually drawn out by the vacuum pump) rather than condensation. $\endgroup$
    – Hobbes
    Commented Jan 9, 2016 at 17:10
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    $\begingroup$ @Hobbes Not necessarily, it can also freeze solid in places you don't want it to inside the craft where it's thermally shielded (shadow far enough from the source of radiating heat would do) or through sublimation cooling or on cryo-cooled surfaces. Point is, you don't want to carry the weather along with you (like Gaia apparently did). And mitigation once in orbit can be tricky, not every surface can be safely baked-off, especially parts that have been carefully engineered to avoid thermal cycling or are sensitive to thermal expansion and other mechanical or even electrical damage. ;) $\endgroup$
    – TildalWave
    Commented Jan 9, 2016 at 17:52
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    $\begingroup$ @Hobbes Apologies, apparently Gaia didn't suffer stray light degradation due to ice, but it was later discovered that detached fibres from its MLI are the most likely cause. I confess, I didn't follow-up on that and assumed that then working assumption was the true culprit. Apparently not, but it was considered, so my point stands that water ice can potentially be a problem and there is a point in making sure there isn't any. $\endgroup$
    – TildalWave
    Commented Jan 9, 2016 at 18:24
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    $\begingroup$ If you store something wet in vacuum for long enough, eventually it'll be completely dry. Here we'd have a room-temp vacuum chamber, so that would make the drying much faster than on orbit in the shade. The main reason for not using a vacuum chamber is that it's way more hassle than needed merely to dry something out. Dry inert gas costs orders of magnitude less than vacuum. $\endgroup$
    – Kuba hasn't forgotten Monica
    Commented Jan 13, 2016 at 20:43

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