No, the wikia codex is intended to mimic the in-game codex, as you will see in its history. This is so that anyone attempting to look up a missing entry can identify it, even if it is a bug. This is most obvious in the chroma effigy entry when I originally added it last year, althought there are other many examples of duplicates being kept to help people identify entries. The in-game codex is sorted alphabetically, it just ranks letters over space, again ordering is important to allow people to identify missing entries. The nullifier entry is formated using the 'notes' formatting as it doesn't create a broken link. When I originally added this to entries (drone, zanuka hunter, vey hek frame for instance), it was to maintain usable links while still keeping the position and name as it appears in the codex. Although creating a new page or variant section for Nullifier Target is possible I suppose, if you wish to fix the link.
Yeah here's the differences I noticed; the cycling bar-laser thing across some of the doors wasn't present in the day mission. The vaults that contained a single Sensor drone at night contained a single Lancer during the day.Those were the only differences I took note of, there are probably others though.