Repository-style updates such as those found in Ubuntu have been used for years and years, and haven’t caused any problems. If its a concern for you, either stop updating, manually download/compile new versions, or make it automatic.
The rest of us don’t really mind.

I really like the icon change. Also, having the icon go grey when apt is running (letting you know you can’t run it again somewhere else until the first one is finished) is great.