Rashi and Tosafos were also cencored.
It looks like the Vilna Shaas itself was edited after the layout, unless they purposefully made it look that way. Where there are large portions taken out the Blatt has more room on bottom. It is not such a big deal to stick in a couple of lines into the layout. You adjust the letter and word spacing.
In France, in the time of the Rishonim they burned cartloads of Sefarim. It is called the Gezeira of Vav Chukas.