Here is where I planned on proposing the idea that Voyager simply renamed their lone Shuttlebay as "Shuttlebay Two" because "Shuttlebay One" was removed at some point during the design phase.
However, there are three instances where Shuttlebay One was mentioned (as opposed to the three where they mentioned Shuttlebay Two), that make it seem like an actual place somewhere on Voyager.
The Enterprise-D doesn't seem to have a "Shuttlebay One", per transcripts, although they have their own "Shuttlebay Two" (15 refs) and "Shuttlebay Three" (2 refs). They have a "Main Shuttlebay", which *might* be Shuttlebay One, but who knows. Voyager never referenced a "Main Shuttlebay" (unlike TNG with its nine references), but perhaps Shuttlebay Two *is* the main shuttlebay, and Shuttlebay One is just some small alcove somewhere (... that the Delta Flyer flew out of, once? I don't know).
Behind-the-scenes info just has "Shuttlebay 2" refer to a maintenance bay or hangar behind Shuttlebay 1.