All hidden achievements are related with the main storyline, so you won't miss them as the game progress unlocks them. All of them are uncovered when you finish the main game.
A Fair Day's Pay - Unlocked after mission Caida Libre.
A Friendship Resurrected - Unlocked after mission Fame or Shame.
Blitzed - Unlocked after robbery in Blitz Play.
Diamond Hard - Unlocked after jeweler robbery..
Small Town, Big Job - Unlocked after bank robbery (The Paleto Score).
Subversive - Unlocked after robbery on Merryweather (The Merryweather Heist).
The Big One - Unlocked after the last robbery (The Big Score).
The Government Gimps - Unlocked after robbery on FIB (The Bureau Raid)
The Moment of Truth - Unlocked after revealing the truth about Brad by Trevor (Bury the Hatchet).
To Live or Die in Los Santos - Unlocked at the end of the game.
Welcome To Los Santos - Unlocked after the first Franklin mission.