Disable user

This is a good practice and would disable the user. I used to do it, and it worked fine.
This will "disappear" the user. All his files will be owned by an unused UID, etc. But it works, and easily reversible.

I would disagree. Although files remain in the system, the user is, de facto, disabled.
You can also change the default user's shell to something like /bin/false or the likes, which will achieve similar effect (noe disabled, but cannot login).  

My disagreement is with commenting out the user.

locking the account with the passwd command is the proper way to disable the user.

Changing the shell is not necessary if the user has been locked using the passwd command.  It is a common practice when you want to allow a user ftp access while not allowing shell access.

Of course if this system is using nis, nis plus or ldap, then there are other considerations, since the intended user may not even be in the local passwd file...

I assume that the original questioner will tell us more.

No NIS or whatever ... just a local machine. What would happen to passwd and shadow file if you type passwd -l username? Will it get deleted? or has somekind of mark telling us that the account has been disabled?

It will put the string;

*LK*

in the shadow file.

Just as a further comment, unless absolutely necessary it is EXTREMELY bad form to manually edit /etc/passwd.  You should go through the proper commands for any changes.

Too many ways to effectively lock yourself including root out of the system.