I have had the same problem for years, for fresh installs, a lot of libraries are not set to auto although I see no reason for them not to. I have been setting auto on all libraries manually, but once or twice I ran into problems because something important was uninstalled thereafter (once it was a pam module I think :( ).
So I'm not sure if it is a good idea to mark every library as auto by hand. If you do, I recommend the following procedure:
- make a complete backup of your system (always a good idea!).
- save a list of installed packages (for example
dpkg -l > installed_packages.txt).
- mark all libraries as auto where you think it's not a problem (risky!) and let aptitude uninstall some of them.
- reboot and see if everything works as expected.
- if not, reinstall all packages that were uninstalled and figure out which were really important.
- If system is unbootable, use the backup.
That being said, I have been doing this for a long time and did not run into many problems. I wish there was an official Debian guide / answer why this is so in the first place, but I have not been able to find one. If anyone has a pointer to something that helps solving this problem / give a better answer I were really grateful myself!