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Mainly because there are other legendaries (Raikou, Entei and Suicune) who are more of a pain to catch. This is because in Silver, these three are roaming legendaries, so you have no warning of their approach and hence can't save prior to battling them. They're also prone to fleeing. Given that, you can save yourself some of the hassle by holding on to your master ball to use on one of these guys.
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