Back then, it was all way more rudimentary than it is now. The hardware wallets we use these days generate a new address for every transaction, but that new address comes from just one private key, so its super easy to generate thousands of addresses and have access to all of them. Now its true that all of these transactions for Satoshi are the block rewards, so they are in 50 BTC chunks, but you're right, how to manage them all? I'm not 100% sure, but when you're doing the mining, the block template that you're using to do all your hashing on for the next block has the coinbase transaction in there which is the address that the block reward, the 50 BTC, will be sent to (you can spend from this address after 100 blocks). Each new block would need a new block template, and I'm not sure how the script worked back then to put this address in there. I guess its possible that he had some way to automatically generate and keep track of all the addresses from private keys, and maybe John has more info on this, but I'm almost guessing the reason they say those coins are lost is because Satoshi probably didn't care too much. He was the only one mining for a while, so those coins likely all just went to random addresses.
You sound convinced that Hal is Satoshi? Edit... I did see a study done on Satoshi's postings, and some were made while Hal for running in races... Jameson Lopp did a great analysis there.
It was Hal who made the first bitcoin transaction by receiving a free stash from Satoshi. But why the heck would he do that? Publicity stunt? For a guy who prefers to remain anonymous, that seems a bit odd.