Why do some shops and houses stay locked during the day?

You mention above that you were waiting at Calixto's - I had the same issue multiple times.

Then I discovered a particular Windhelm quest - turns out the shop owner is occasionally "out" doing other things because of the related series of events. Once you start the quest line, this also limits the shop's hours of operation. I won't spoil you with the name of the quest, but I'd recommend just shopping elsewhere.

One possibility, something which I encountered, if you're waiting while the locked popup is open, the locked information will not disappear. Look away from the door and try again.

For me, this always (almost) happen with Fletcher in Solitude.

If I wait until mid day and try to enter the store it's always closed. The only thing that works is to wait one more time (just one hour is enough).

Then the shop should be open.

I have no idea why this is the case though...