Both sentences are grammatically correct but there is an issue with cas which is odd here and make them unidiomatic.

If we replace it with choix which works better, we have:

Quel est le choix maintenant ?

which is correct and means:

What is the choice now?

and

Qu’est-ce que le choix maintenant ?

which is still correct but unlikely to be used as it means:

Qu’est-ce, le choix, maintenant ?

which translates to:

What is “choice” now?

i.e.

How would you define “choice” now?

while I guess the expected meaning is What’s the choice now?.

Note: Qu’est-ce que le… is usually replaced nowadays by qu’est-ce que c’est que le… or in spoken French by c’est quoi le… The latter can be used to mean either “what’s the..” and “what means…”

I
The problem is purely one of context and of confusion between the meaning of “quel” and the interrogative locution “qu’est-ce que” (considered to be a pronoun in French grammar today); both forms are perfectly idiomatic; the first will fit a common context, the second will be rare as the context it entails is rare for the word “case”, and so we are not used to hear it or read it.

The first question is asking which element among a certain more or less known number of elements is the one that is relevant.

(TLFi) [Quel, adj. interr. + subst. interroge sur l’identité, rarement sur la qualité]

• — Quel est le cas maintenant?

  — C’est le cas que l’on a traité hier.
  — C’est le nominatif.

The second question is asking what is the nature of a certain element named by a word of which, in fact, the meaning is what is being asked.

• — Qu’est-ce que le cas maintenant ?
  — Le cas maintenant c’est ce que ça a toujours été, le nom de la fonction grammaticale du nom dans la phrase, rien de neuf. (1)

We can notice that numerous nouns commute with “cas” naturally when “maintenant” is removed.

• Qu’est-ce que le Web ?
• Qu’est-ce que la télévision ?
• Qu’est-ce que la course à pied ?
  …

Adding “maintenant” restricts the context enormously, wherefrom the apparent unnaturalness. However, the special instance of the pupil that believes that the name “cas” in the context of latin grammar could have more than one meaning as his/her “maintenant” points to a possibly new acceptation ((1)), makes it unmistakable that the form is idiomatic.

II Could we use the second sentence to render the exact same meaning carried by the second one?

If we consider the commutation examined above we see that this is never the case. Would the addition of an adverbial change that (“maintenant”)? I think it wouldn’t, I see no possibility of that.