That’s a plus too. An “aptitude dist-upgrade” is really fast.
For example, for our deployment, we rely on softlinks and uwsgi robust reload behavior to avoid losing requests. I've seen many devops who were using hg update/git update as a way to "deploy" (arg!), but I'm not sure about the behavior of deb/rpm.
And you’re right: replacing files of a running application can lead to all kind of weirdness. I’d even prefer to lose some requests than to risk that.