I vaguely recall seeing an explanation as to why this is the case... I seem to recall it was because if the wallet.dat was fully encrypted (and not just private keys) you would need the password simply to open the wallet file at startup, and that this would be problematic when using "bitcoind", as it doesn't have a GUI to prompt the user for input etc.

At the end of the day... the private keys are protected (the most important thing) and if someone has access to be able to read your wallet.dat... you've probably got bigger problems that their ability to see your transactions/balances etc.