That got me curious, so this morning I went through all the PopTop locos (including diesel and electric) and it turns out there's only one other locomotive that has an _Omni01.3dp in its bunch of files: the Class 6E electric.
Ok, weirder and weirder. Next thing to do is check out the structure of the files. It appears to be identical to a single light file. IOW, the basic "glow balls" that are used for things like firebox or instrument glow inside the cab, as opposed to the "double light" files that are used for things like a headlight, and which have an extended beam as well as the smaller lens glow.
The one for the #999 Eight Wheeler turns out to be positioned inside the cab, about 10 inches behind the upper backhead and offset about 16 inches to the left. This indicates it was probably meant to be a light of some sort. It's coded it to be pure white (RGB 255, 255, 255), with a nominal glow radius of 2 inches, but it's not visible when viewing the locomotive at night.
I haven't tested the one on the Class 6E yet, but I would assume that is non-functional as well.* It appears that these files were originally intended to take the place of the usual single light files (ie: an omnidirectional light) but were deprecated during development. My guess is they found they could make them all work while just being called _Light*.3dp, and this saved them having to think up a name for the other sort of lights.
Bottom line: If you happen to spot an _Omni01.3dp file while messing with locomotive files and are wondering what on earth it does, the answer is it doesn't do anything. It's superfluous, and can be removed without adverse effects.
*Just checked, and as expected the Class6E_Omni01.3dp is also non-functional.