The manual merely says "Dumb. Tough. Flies. On Fire. 'Nuff said." They weren't translucent in the original game (but, to be fair, nothing was really). So, making them translucent in a source port (usually as the default setting) is a move away from the original appearance.
I mean, I get that their name and general appearance implies that they might be spooky, ghostly kind of things but they are also mostly bone and can stop a shotgun pellet or bullet. I can see that making the flames translucent is quite cool but the bony parts? That's always struck me as a bit odd.
My memory on this isn't the clearest but I think it just started with one of the early source ports (probably to show off the new, cool translucent effect it could do) and the others just dropped into line behind.
In addition, and only slightly related, I remember that early versions of Legacy had quite a cool trick where certain items could be flagged to use a special effect (perhaps a special palette hack?) where parts of the actor were drawn translucent but other parts were not. e.g. the flaming torches were set to have translucent flames but the stands were fully opaque. I'm not sure if the lost souls in Legacy got this treatment or not.
[edit]
FWIW, here's a couple of screenshots in Legacy 1.28 showing the effect with torches.
Spoiler:And it would seem as if it was applied to lost souls too:
Spoiler:Although, of course, the logic breaks down because when looking at a lost soul from behind, you should be able to see through the fire to the bone but because there isn't actually any sprite to see there, you just see right through to whatever is behind in the world.
Spoiler: