Whether you beleive in them or not in real life, in the B5 Universe, they do exist.
Are you sure? Did the story of "Babylon 5" present us any central authority, anyone possessing absolute truth... to invalidate and/or resolve the contradictory views of its characters -- presented from multiple viewpoints and levels of experience?
No... the storyteller who told this story did not invest anyone/anything within the story with such authority. Among the reasons why I like this show... was not rushing to close questions which are open.
Nothing in "Babylon 5" actually established the existence (or "correct" definition) of soul. Even the multiple episodes and one telemovie heavily intertwined with this issue.
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What did Soul Hunters capture and keep? One could call them personalities instead of souls. But as mentioned, that would descend into semantics, since I cannot define what another person *considers* a soul.
What a Soul Hunter might call "soul", someone else might consider a fairly complex and dynamic (but hardly inexplicable) data structure.
Those might be mere stored personalities (even incompletely stored ones, given a probable transfer from analog to digital) -- stored in an environment which has detrimental effect on their sanity.
As opposed to natural personalities operating in their native body (or artificial personalities constructed without ever having one, referring to the artificial intellect called Sparky, and "Deconstruction of Falling Stars").
As for the visions seen by Lochley, Garibaldi, Lennier and some others... they might well be the creation of a sufficiently complex hallucinogen -- especially when combined with other technology.
We never learned if the difficult-to-deceive robotic eyes of the station saw what our characters saw -- or whether the even keener eyes of a Vorlon or Shadow would have seen through the entire situation.