El cielo está casi negro con tantas nubes.

Estar is used for temporary or changing states, and for physical appearance that can change.
The sky is not always black; it’s just dark right now because of the clouds.
So El cielo está casi negro = The sky is (currently) almost black.
Ser would suggest a permanent or defining quality, which doesn’t fit normal sky color.

Yes, but it would mean something different and sounds unusual.
El cielo es casi negro would describe the normal or typical color of the sky in a place, for example: a planet, a painting, or a heavily polluted city, where the sky is usually almost black.
In everyday weather talk, you want a temporary state, so you use está.

Casi is an adverb meaning almost / nearly.
Here it modifies the adjective negro, softening it:

• negro = black
• casi negro = almost black, nearly black, not completely black
  Grammatically, you can think of it as part of the adjective phrase casi negro after está.

The natural position here is: El cielo está casi negro.
You generally put casi right before the adjective or adverb it modifies.

• ✅ El cielo está casi negro. (normal, natural)
• ❌ El cielo casi está negro. (sounds wrong or very strange in this context)

El cielo casi está negro would be interpreted as casi modifying está, and native speakers wouldn’t normally say it that way about color.

Adjectives agree with the subject of the verb, not with the cause of the state.
The subject is el cielo (masculine, singular), so:

• el cielo → negro (masc. sg.)

Nubes is just part of the prepositional phrase con tantas nubes explaining why the sky looks that way; adjectives do not agree with nouns inside such phrases.

Cielo is masculine because that’s its grammatical gender in Spanish: el cielo.
Most nouns ending in -o are masculine (el libro, el vaso, el cielo), although there are exceptions.
There isn’t a logical reason beyond usage and vocabulary; gender is something you generally just memorize with each noun.

Both indicate a large quantity, but:

• muchas nubes = many clouds / a lot of clouds
• tantas nubes = so many clouds, so much (emphasizes a surprising or remarkable amount)

In this sentence, tantas nubes highlights that the number of clouds is great enough to almost turn the sky black.

Tanto is a quantifier that agrees in gender and number with the noun it modifies:

• masc. sg.: tanto dinero
• masc. pl.: tantos coches
• fem. sg.: tanta lluvia
• fem. pl.: tantas nubes

Here, nubes is feminine plural (la nube / las nubes), so you must use tantas.

In Spanish, when you talk about an indefinite quantity of plural nouns (many clouds, so many clouds), you normally omit the article:

• tantas nubes
• muchas nubes
• pocas nubes

Las tantas nubes would sound odd and would suggest a specific, known group of clouds that has already been clearly identified in the conversation. In general descriptions like this, you don’t use the article.

You could say por tantas nubes, but the meaning changes slightly:

• con tantas nubes = with so many clouds (they accompany the sky; descriptive)
• por tantas nubes = because of / due to so many clouds (focus on cause)

Con tantas nubes sounds more neutral and descriptive for this kind of sentence.
Por tantas nubes emphasizes that the clouds are the reason the sky is almost black.

Yes, it’s understandable and grammatically correct:

• El cielo está casi negro por las nubes. = The sky is almost black because of the clouds.

However, con tantas nubes is a bit more vivid and visual (you imagine the sky full of clouds), while por las nubes is more explicitly causal and less descriptive of quantity.

Yes, you can say: El cielo está casi oscuro con tantas nubes, though casi oscuro is a bit unusual (you’d more often hear muy oscuro).

• negro = black (very intense darkness)
• oscuro = dark (not necessarily black, just not bright)

Casi negro implies it’s extremely dark, nearly black.
Muy oscuro would suggest it’s very dark, but not to the point of being almost black.

Yes. A Spaniard might say things like:

• El cielo está casi negro con tantas nubes.
• El cielo está casi negro, parece que va a llover.

It’s a natural, everyday way to describe a sky that looks very dark because it’s full of clouds.