What are the hidden bonuses/penalties of hamlet stress buildings?

A list of possible negative and positive consequences after using the Tavern is listed on the Darkest Dungeon Wiki. The Abbey has a similar list. The Sanitarium however does not seem to have additional effects apart from the upgrades.

My source here states that there are possible side effects most often negative but a chance to be positive. The Activities wiki's are found here:

• Meditation
• Flagellate
• Pray
• Gamble
• Drink
• Visit the Brothel

A full list of Quirks can be found here.

And the Hamlet wiki is found here.

The positive and negative side effects of visiting a place are called quirks.

The Tavern and Abbey have positive and negative quirks that can be randomly gained by participating in the aforementioned areas. For example, by meditating, a hero could possibly achieve a Balanced quirk, which is a positive quirk that gives them +15% move resist. Likewise, however, they could also achieve a negative quirk from the same activity, such as Calm, a negative quirk gained by meditation that makes the hero deal -15% DMG on the first round.

To answer about the Sanitarium regarding quirks, no, you cannot receive positive nor negative quirks by visiting or interacting with the Sanitarium. However, you may use it to manage your quirks by removing the negative quirks and/or keeping the positive ones in exchange for payments of gold.

I hope these provided details are satisfactory. If not, please ask any questions and I'll do my best to answer right away.

Visiting the Abbey or Tavern has a 37.5% chance of a positive or negative side effect occurring. The Sanitarium doesn't have a chance for any side effects of occurring, but there is a chance that any hero being treated for a disease may have multiple diseases cured, instead of just 1. I'm not sure on the exact chance, but at least with upgrades, it seems to happen fairly regularly. I've had multiple heroes who have had all their diseases cured with one visit to the Sanitarium.

The side effects you can gain from the Abbey or Tavern will vary between locations, but they have a few things in common.

For starters, every location has a chance to result in the character gaining a quirk which will result in them either never being able to visit that location again (i.e. Love Interest) or only being able to visit that location (i.e. Deviant Tastes). Of note the the Penance Chamber doesn't have a dedicated "will not visit" quirk, but instead will grant Faithlesss, which forbids a character from visiting the cloister and the penance hall. Some locations also have a chance of granting the character some other quirk, either positive or negative (full list below).

Another effect shared among all locations is a chance for the character to go missing for 1-2 weeks, meaning they can't be sent on quests or to treatment facilities. Additionally, with the exception or the Transept, every location has a chance of the character staying for an extra week of treatment. This extra week is free, so if the heroes stress was really high, this can actually be a good thing.

Most locations have a chance of granting the hero either a positive of negative stat bonus until their next quest, such as +6 speed (Brothel) or -10 ACC (Tavern).

A few locations also have a chance of the player gaining or losing some gold, or gaining or losing some trinket. Trinkets can only be lost from the gambling hall and brothel, and based on my own experience and some reading online, the trinket will be taken from your inventory. It might be taken off the visiting hero if possible, but I can't confirm this. Either way, the chance of losing a trinket is roughly ~2.5% when visiting either location.

The complete list of side effects can be found below. For details percentages of each location, you should consult the wiki.

Abbey

• Cloister
  • Positive quirk: Balanced, Mediator
  • Negative quirk: Enlightened, Unquiet Mind, Calm
• Transept
  • Negative quirk: God Fearing, Witness
  • Receives -20% stress
  • Gain a trinket
  • Lose 1000 gold
• Penance Chamber
  • Negative quirk: Faithless, Flagellant
  • Receives +20% damage or -25% bleed resist

Tavern

• Bar
  • Negative quirk: Resolution, Tippler
  • Receives +10 HP, -10 ACC, or -5 DODGE
  • Lose a trinket or 500 gold
• Gambling Hall
  • Positive quirk: Skilled Gambler
  • Negative quirk: Known Cheat, Gambler, Bad Gambler
  • Gain 2000 gold or a trinket
  • Lose 1000 gold or a trinket
• Brothel
  • Negative quirk: Love Interest, Deviant Tastes
  • Disease: Deviant Tastes
  • Gain +6 speed, -25% stress, -5 speed
  • Lose 750 gold or a trinket