When Weir come under the influence of the entity possessing the Event Horizon, is it himsuccumbing to insanity? Or is it the Event Horizon itself possessing him and speaking through him?
We'll never know, but the novelization implies that the Weir is dead, and an entity from Hell is using his form and voice. In the final fight, the entity spits and says that Weir (in the third person) was weak.
Likewise, is Justin merely acting deranged from his exposure to the other realm? Or did the entity possessing the ship temporarily possess him and speak through him? His stunned reaction when he discovers himself in the air lock suggests the latter.
In the final scene of the film, is Starck merely having a nightmare? Is she experiencing an anxiety attack due to the trauma she just experienced? Or are the remains of the Event Horizon still possessed and tormenting her?
The ambiguous nature of that is probably the point.
Related to this, however, is the fact that in her "nightmare" she sees Weir as he looked after the ship brought him back...something SHE DIDN'T KNOW...
Although this part apparently had more ambiguity in the original cut: part of one cut scene has the scar-covered Weir crawling down after Starck and Cooper after Starck is flushed down the ladder by the blood tidal wave.
I see no reason it couldn't be all three. That damned ship is evil as hell.
The way the spiked doors ominously close on the survivors and the rescue crew at the end seem to imply that the remains of the Event Horizon are still possessed and functioning.
So why is this a Warhammer 40k movie? Might it be possible that the creators never heard of Warhammer?
Event Horizon is not related to the Warhammer 40000 universe at all. It's just a joke that 40k fans like to tell due to similarities. Ship makes a Warpjump... uh, I mean experimental FTL jump, which causes the ship to fly into the Warp... uh, I mean Hell, and makes the crew fall to Chaos... uh, I mean go utterly batshit, and then the ship gets possessed by daemons... uh, I mean generally becomes this weird sentient place that drives everyone mad, and then Weir gets possessed by a daemon... uh, I mean, well you know.
It's not just the mechanical function of things; that alone is enough to make the Doom connection, since Doom is very light on plot, but not 40k, since 40k has a lot more to dive through than "mechanics of FTL travel." What sells the idea is the fact that, beyond that, the film has an extremely similar design aesthetic to 40k; the note on the YMMV page that it wouldn't be hard to fool a 40k fan who's never seen heard of the movie into thinking it's intended to be 40k isn't much of an exaggeration, if at all. No, no one thinks it's supposed to be a 40k film, but you wouldn't have to change anything for it to be one.
Within a minute a crew member can understand that it's Latin in the Event Horizon's last transmission, but the entire accident investigation team that Earth presumably would have had in "The largest space accident ever" no one noticed?