Ya es hora

Ya es hora means It's time. Here are some examples:

• Ya es hora de irnos. Es hora de que nos vayamos. It's time we left. We should be going (now). Note that you can use either the infinitive or the subjunctive.
• Ya no son horas. It's too late in the day to be doing that. (to be making so much noise)

As you can see, this expression can be used when an unrealized event should have happened earlier.

Qué horas

In contrast, Qué horas is used when something happened later than you wanted. ¡Qué horas son estas! ¡Qué horas de llegar son estas! ¡Qué bonitas horas de llegar! It's late. You should have gotten home earlier.

A estas horas means at this late hour. Llegar a estas horas. To come home this late.

Se te llegó la hora

In a telenovela, I heard: Se te llegó la hora. Today's your day to die. More generally, it could mean your time's up.