Of course, if you're logged in as root, you don't have to type the password at all, as it's saved in /root/.my.cnf. The only time you need it (or an equivalent) is for setting up something like phpmyadmin. For anything else, you should be creating separate users for each database/app, so that a compromise of one won't compromise your whole system.
I agree, the long password is a bit of a pain, but it's used rarely enough that it's not much of an issue (at least for me).