Some sample sets have multiple recordings of the same note. Hauptwerk can randomize which of those samples will be used. Using this feature increases the realism in that notes tend to vary slightly with the wind supply fluctuations. This also reduces ear fatigue because you do not hear the same sample repeatedly.
Some samples have multiple recordings of the ambient pipe reverb. These "release samples" typically sample a staccato note reverb, a medium length reverb and a long held note reverb. Having multiple release samples allows users to maintain the clarity of the sound while playing fast, contrapuntal music.
The alternative is to have, for example, a 10 second reverb tail for each note regardless of how long you play that note. If you are playing a fugue for instance, this will not only turn your performance into a sonic "mush", it will also bog your computer processor down as it tries to process all of those needless 10 second reverb samples.
Hauptwerk allows users to compress the samples so that they take up less room in RAM than uncompressed samples. While the encoding maintains the same sound quality of an uncompressed sample, it takes much more processing power to uncompress and play the samples than to play an uncompressed sample. If you have lots of processing power but are short on RAM, you might wish to use this feature