I don't know why /var/log/apt gets missing in your particular case. The most common reason is using tmpfs for /var/log which is a usual practice for SSD-based systems. Since SSD-based systems get more and more common (especially thanks to Asus Eee PC :-)) I think it would be nice to have correct operation with /var/log/apt missing (just create it if it doesn't exist).
I don't know why /var/log/apt gets missing in your particular case. The most common reason is using tmpfs for /var/log which is a usual practice for SSD-based systems. Since SSD-based systems get more and more common (especially thanks to Asus Eee PC :-)) I think it would be nice to have correct operation with /var/log/apt missing (just create it if it doesn't exist).