I vary my methods.
Rifle hunting ammo with exposed lead noses or self defense rifle ammo with expose lead noses gets left in the box and packed so the ammo won't get damaged.
Get me into something like ball 45acp and it is loose in an ammo can for space reasons.
This can sometimes vary by ammo can purchases. In the past I would hunt for deals and buy cans here and there. If academy or someone will sell 50 cal cans for 10 bucks a pop shipped, and I pay tax, I will get another dozen or so this year.
Anyway, when ammo can rich, sure ammo can stay in the boxes. When ammo can poor, ammo comes out of boxes. Generally when buying another dozen or so ammo cans I have to redo things a bit to make room anyway and it is not a big deal to open ammo cans to dump out ammo if there are in boxes. I can usually tell from my label on the can if they are loose or boxes, loose puts a lot more in the can.
I am also known to sell ammo sometimes if something changes in my thinking. I had a ton of 357 mag ammo but once I sold my last 357 mag revolver the ammo went away as well.
So in some cases I might have stuff boxed cause I am considering options.
I have a few calibers I am set on. Not changing things. So not as worried about dumping those out. But some of the others, might be a tad concerned and might keep them boxed.