Text translations and upgrading WordPress

I recently received some helpful advice how to translate WordPress text strings:
http://stackoverflow.com/questions/21932828/translating-wordpress-which-naming-convention-should-i-use-when-defining-the-la

But I still don’t quite understand why using a language file is bad practice? The Codex even advises it in this article:
http://codex.wordpress.org/Translating_WordPress

If I go down the language file route, are my changes lost if I upgrade WordPress?

Hoping someone can explain? Thanks in advance.

[ No bumping please. ]