One of the biggest optimizations it offers is shrinking the size of the classes by obfuscating the names. If you're obfuscating the names anyway, there's no reason that the names have to be the same length.
"hn$z" is a heck of a lot smaller than "tld.organization.product.domain.concern.ClassName"
So we're not talking about runtime performance, but some minor improvement in loading times? I assume that once the JVM has read the bytecode, it has its own efficient in-memory structures to track references to classes rather than using a hash map with fully qualified names as keys
Proguard was heavily influenced by the needs of early Android devices, where memory was at a real premium. Reducing the size of static tables of strings is a worthwhile optimisation in that environment
Even a hash map with fully qualified names as keys wouldn't be so bad because Stirng is immutable in Java, so the hash code can be cached on the object.
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