Even stolen items I'm not carrying at the moment, like in chests at my home?

I ask because when I first started playing the game, I kept getting a high bounty and when I finally paid it off instead of just killing guards, they made me give back EVERYTHING I stole that I was carrying.

Since then, I had re-rolled a character and I've been extremely careful when commuting crimes so I have zero bounty. However, I'm about the start the DB quests and I'm reading that getting a bounty is unavoidable in some situations- people suggest to just pay the bounty.

BUT will this make me have to give back the 100s of stolen items I have stored in chests at one of my homes?

Only what your carrying.