Cydonia is actually a region on Mars - the name derives from here and is not actually made up. Sidonia seems to be an alternative spelling for this.
As for the "knights" bit, the region is best known for the face-shaped landmarks that were discovered by the Viking Orbitors, It is very likely the "Knights" refer to these faces, which strike a resemblance to tapestry and stained glass depictions of medieval knights:
Some commentators, most notably Richard C. Hoagland, believe the "Face on Mars" to be evidence of a long-lost Martian civilization along with other features they believe are present, such as apparent pyramids, which they argue are part of a ruined city.
The region has been featured in more than these two mediums and in fact has inspired episodes of the X-Files, Final Fantasy IV, Invader Zim and more.
There doesn't appear to be a connection to the two works apart from the names, which may have differing spelling to avoid lawyer conflicts, for search engine & catalogue uniqueness, because of mistranslation, or a variety of other reasons.