Several users (including the writer of this article) then proceeded to have Steam redownload any missing redistributable installer, the cause for the 100-350MB updates, though some users have reported higher sizes for some games. Starting a game for the first time over Steam always has a setup process that involves checking to see if either Visual C++ or DirectX components are up to date for the game that is being played, and installing any missing components if they are not present or up to date. This is a common practice for anything downloaded over Steam that use these to function. The reason for these "updates" was actually that these updates were deleting redistributables for Microsoft Visual C++ and DirectX in games that they were packaged with (the writer of the article has confirmed this himself). There's a reddit thread and several threads on the Steam forums about the issue happening.
In some cases, the empty updates were followed by the few hundred megabyte updates. This appears to be the common consensus as several users logged into Steam today to find out that a majority of their library were either downloading empty updates with no size, or downloading updates that were usually slightly above 100MB but have gone over 300MB in size in some instances.