Vincent wasn't joking, Heather was actually killing people
I definitely don't think every monster in SH3 was an actual person but there are many things that make what he say sound reasonable.
1 - The "monster" who killed Harry is sentient and he follows Claudia orders, also since the place where they lived wasn't a haunted town like Silent Hill shouldn't a monster like that be unable to exist there?
2 - Leonard also looks like a monster but he's also fully sentient, talks like a normal person and also Claudia was devastated by his death, if he really was that horrifying monster why would she be sad over it
3 - The cultists are very much still present in the church, the church definitely doesn't seem abandoned like the hospital or the amusement park, and yet we don't see any human there other than Claudia and Vincent, to me this one is the only place where most of the monsters are actual people
Why does Heather see them as monsters? I'm not sure, maybe she was so blinded by revenge the way she saw people got distorted, or ever since Claudia forced her to be impregnated with god in the mall she also started seeing a distorted view of reality
(And in Heather's defense though all of them attacked her first)