Learn Portuguese (Portugal): Que horas são agora?

In English, we ask 'What time IS it?' using the singular. In Portuguese, you are literally asking 'What hours ARE they?'. Because time is usually more than one hour, you must use the plural noun horas and the plural verb são (from the verb ser).

Is it ever correct to ask for the time using the singular é?

Yes, but Que horas são? is the standard way to ask for the general time. You might occasionally hear the singular Que hora é? if the speaker suspects it is exactly one o'clock, midday, or midnight (which use singular verbs), but sticking to the plural question is always the safest bet.

Why use Que instead of Qual for 'What' in this sentence?

When 'what' is followed directly by a noun in Portuguese (like horas), you almost always use Que. The word Qual is typically used when you are asking 'Which one?' out of a set of options.