Umm.. That's actually the way that the messages are stored internally. Inside the message store, each of those messages to the 100 recipient in each store only occupies a single row in the underlying database.
But even though Exchange is a REALLY good email system, I don't know ANYONE who would recommend that you put all 55,000 Microsoft employee's on the same email server, especially back in the Exchange 5.5 days. At an absolute minimum, this single server would represent a massive single point of failure for the entire corporate email system.
There are multiple servers, and the Bedlam DL3 distribution list went to users on several servers. And as long as the message had to go to multiple servers...