Debatable--the main character is the only one to survive from an excommunicated brotherhood and can fight (among many other people) the person who killed him. However, this lore is only revealed in comics and it's otherwise left vague why the main character is doing what he's doing.
The "Good" ending feature the player character sacrificing themself. The character Viridiana can sacrifice herself to heal the player character during a boss, although this is after a few times of doing it and is entirely optional.
Some NPCs, such as Deogracias and Redento wander through different areas in the game, although this is more or less by choice, and whether or not they're homeless isn't discussed. I'd say "yes" because they might remind someone of that.
Redento regularly walks through rough terrain barefoot as part of his pilgrimage, although his feet aren't shown in detail and he only mentions offhand how his feet ache.
There *is* a hospital, but it's a safe zone in the central hub town, and you can collect herbs the doctors need to make medicine. That said, in the background, there's lots of sick people with some really nasty-looking wounds.
Nudity is fairly frequent, although the game is pixelated. Though some is more detailed such as the cutscene where the lady of 6 sorrows is introduced.