Given that the Vortex is essentially the warp intruding on reality, I have two questions:
1. How do ships travel the void? It's said that Navigators are sent screaming (hence the Screaming Vortex) once they open their third eye. Does all void travel within rely on Daemons or Sorcerers? What is the nature of these sorcerers? Are there no chaos navigators, like Octavia in Soul Hunter who has to take the Night Lords back to the Eye of Terror.
2. Do ships have geller fields? I doubt the forces of the warp care if the local traffic is heretics: a meal is a meal! So how can anyone actually travel through the void - particularly as the warp openly intrudes on reality within the Vortex - safely? In fact how come the worlds of the Vortex, even the Gloaming Worlds, aren't all a mass of daemons and slaughter?
From the description of the Warp Guide, Rogue Psykers, page 118 and 119 of The Navis Primer:
"A Warp Guide unlocks the ability to traverse the Warp through Human sacrifice, attracting Daemons to lead the vessel through the Warp."
"By treating with Daemons and paying a tribute in blood and souls…"
"Often, ships led by Daemons find themselves lost within the twisted depths [of the Warp] with no means of escape and no sign of their [Daemonic] guides but a faint cackling."
Warp Guides possess a special ability, known as Blood Sacrifice: "While they are not Navigators in the traditional sense…Warp Guides can navigate great voidships through the Warp using guile, their few innate psychic abilities, and the unpredictable aid of the denizens of the Warp."
The Navis Primer also sheds (some) light on the "shrouded", Renegade, or cursed Houses of the Navigators. House Nostromo, the fate of which is tied (perhaps forever) with that of the Rogue Trader Dynasty of Haarlock. The Renegade House of Typhon, known to have associations with a variety of undesirable factions within the Imperium's vast institutions, notably Inquisitors of a decidedly Radical mindset (some of whom were excommunicated). House Malaspina, whose shrouded past traces its tenebrous origins to the time of the Horus Heresy and whose Navigators are not accepted on the vessels of First and Second Founding Astartes Chapters. It is entirely possible that certain ancient Renegade Houses have continued in their service to those who followed the Ruinous Powers into damnation along with the Traitor Legions. It is also likely those same Renegade Houses are a most precious resource to the Chaos-tainted warlords who ply void and aethyr.
The (excommunicate) Phaenonites could indeed possess some malefic techno-sorcerous device that makes the use of Navigators redundant. The mini-adventure concluding the Dark Heresy publication The Lathe Worlds touches upon this very subject.
I read (most of) Soul Hunter, and while I found it to be lackluster and cliche, I believe the Navigator you reference, Octavia, is a prisoner of the Night Lords, captured from another vessel for the very purpose for which she was born. Thus it might be assumed that Navigators may in fact guide voidships against their will.
I would postulate that, where possible and affordable, all vessels traversing the Vortex, whether in the Warp or otherwise, do in fact possess Gellar Fields. As you say, the denizens of the Warp make no distinctions between the faithful and the heretic. Again, The Navis Primer suggests that mass recitation of baleful dirges and the copious offerings of blood sacrifices may very well replace the Gellar Field.
Rarely do I ascribe literal meaning to "flavor" text within 40K RPG publications. If in fact it is stated somewhere that Navigators "are sent screaming" I would take that merely as an indication of the dread nature of the Vortex and its environs. Likewise, though the Warp intrudes upon worlds of the Vortex, I believe we are meant to suspend the notion that these incursions are "all or nothing" occurrences. Hence the "flavor" text given for each individual world within the Vortex; some are spared its worst, others are absolutely steeped in its blasphemy.