Estas entute kvin krateroj.

No subject is missing. In Esperanto, estas can be used like English there is / there are to state that something exists or is present.

So:

• Estas kvin krateroj. = There are five craters.

Esperanto does not need a separate word like English there in this kind of sentence.

Entute means in total, altogether, or all told.

So:

• Estas kvin krateroj. = There are five craters.
• Estas entute kvin krateroj. = There are five craters altogether / in total.

It adds the idea of a total number.

Because krateroj is plural.

In Esperanto:

• -o = noun ending
• -j = plural ending

So:

• kratero = crater
• krateroj = craters

Since the sentence says five craters, the noun must be plural.

Esperanto has no indefinite article like English a/an.

It does have a definite article, la, for the, but it is only used when needed.

Here, the sentence is just talking about a number of craters in general, so no article is necessary:

• kvin krateroj = five craters

If you said la kvin krateroj, that would mean the five craters.

Numbers in Esperanto normally do not change form. Kvin always stays kvin.

Examples:

• unu kratero = one crater
• du krateroj = two craters
• kvin krateroj = five craters

The noun changes for plural, not the number.

Yes, Esperanto word order is fairly flexible, although some orders sound more neutral than others.

The most neutral version here is:

• Estas entute kvin krateroj.

You could also see:

• Entute estas kvin krateroj.

Both mean essentially the same thing. The first version is very natural for introducing the existence of something.

Because it is not a direct object.

The accusative ending -n is usually used for direct objects or for certain expressions of direction. In this sentence, kvin krateroj is what exists; it is not receiving an action.

So:

• Estas kvin krateroj. = correct
• Estas kvin kraterojn. = incorrect

Yes, estas is the present-tense form of esti and it does not change for singular or plural.

Unlike English, Esperanto verbs do not agree with the subject in number or person.

So all of these use estas:

• Mi estas = I am
• Li estas = he is
• Ili estas = they are
• Estas kvin krateroj = there are five craters

Normally, no. Here you should just say kvin krateroj.

The word da is used after words that express quantity in a more measure-like sense, such as:

• multe da akvo = a lot of water
• kilogramo da pomoj = a kilogram of apples

But ordinary numbers usually go directly before the noun:

• kvin krateroj = five craters

So da is not needed here.

Entute is an adverb.

Many Esperanto adverbs end in -e, and entute modifies the whole statement by adding the sense altogether / in total.

Compare:

• bona = good
• bone = well

Similarly, entute functions adverbially, not as a noun or adjective.

It is natural Esperanto.

A sentence like Estas entute kvin krateroj is a normal way to say There are five craters in total.

It sounds straightforward and idiomatic:

• Estas... introduces existence
• entute adds altogether / in total
• kvin krateroj gives the quantity and noun

So a learner can safely use this pattern in similar sentences.