Has to be someone close to him who knew about both. I seriously doubt someone compromised ledger’s security and only stole $40k.
It's literally no one close to him. Please take that as a fact. The paper with the seed words was written a few years ago. It has been hidden since. I'm willing to bet we'll be hearing about more people getting their wallets wiped clean.
How good is the hiding place? Both in terms of security (eg. a rock outside your house vs a safe deposit box) and obscurity (eg. on your desk vs buried in a field in the middle of nowhere).