Mater dicit se non crudelem, sed clementem esse velle, etiam cum pueri culpam fateri timent.

Because se is the reflexive pronoun. It refers back to the subject of the main verb, which is Mater.

• Mater dicit se ... velle = The mother says that she wants...
• Here, she means the mother herself, so Latin uses se.

If Latin used eam, that would normally suggest some other woman/girl, not the mother.

After verbs of saying, thinking, knowing, and perceiving, Latin very often uses an indirect statement construction:

• subject in the accusative
• verb in the infinitive

So:

• Mater dicit se ... velle = Mother says that she wants...

This is a standard Latin pattern. English usually uses that, but Latin often uses the accusative-and-infinitive construction instead.

They are doing two different jobs.

• velle is infinitive because it is part of the indirect statement after dicit.
• esse is infinitive because velle normally takes an infinitive complement: to want to be.

So the structure is:

• dicit = says
• se velle = that she wants
• esse clementem = to be merciful

Put together:

• Mater dicit se ... esse velle = Mother says that she wants to be...

Because they agree with se, and se is accusative.

In an indirect statement, the subject of the infinitive is put in the accusative. Any predicate adjective describing that subject also goes into the accusative.

So:

• se crudelem esse = that she is cruel
• se clementem esse velle = that she wants to be merciful

If this were direct speech, the adjectives would be nominative:

• volo crudelis / clemens esse would be incorrect as stated, because predicate adjectives with esse should match the subject in nominative:
• volo crudelis? No.
• Correct direct idea: volo clemens esse = I want to be merciful

Since the indirect statement uses se, the adjectives become crudelem and clementem.

This is a very common Latin contrast pattern:

• non ... sed ... = not ... but ...

So:

• non crudelem, sed clementem = not cruel, but merciful

Latin places non before the thing being denied, and sed introduces the correction or contrast.

In a very literal grammatical sense, yes: se is the subject of the infinitive, so it is like herself.

But in natural English, we usually just say:

• she wants to be not cruel, but merciful or better
• she wants to be merciful rather than cruel

So although se is explicitly present in Latin, it usually does not need to be translated as herself in normal English.

Here cum means when, in a straightforward temporal sense:

• etiam cum pueri ... timent = even when the boys are afraid...

In that use, cum commonly takes the indicative.

If cum introduced a more circumstantial or concessive clause, especially in more literary Latin, you might expect the subjunctive. But here the sense is simply temporal:

• even when the boys are afraid

So timent is perfectly natural.

Etiam cum means even when.

• cum = when
• etiam adds the sense of even

So the whole phrase adds emphasis:

• even when the boys are afraid to admit their fault

It shows that the mother wants to be merciful not only in easy situations, but also in difficult ones.

Because pueri is the subject of timent.

In the clause:

• cum pueri culpam fateri timent

the boys are the ones doing the fearing. So:

• pueri = the boys
• timent = are afraid

That is why pueri is nominative.

It means to admit/confess a fault or to admit guilt.

• culpam = fault, blame, guilt
• fateri = to admit, confess

So:

• culpam fateri timent = they are afraid to admit their fault or = they are afraid to confess their guilt

Because fateri comes from fateor, which is a deponent verb.

A deponent verb:

• has passive forms
• but an active meaning

So:

• fateor = I confess / admit
• fateri = to confess / to admit

Even though the form looks passive, the meaning is active.

Latin word order is much more flexible than English word order. The endings tell you what each word is doing, so Latin can move words around for emphasis.

Here the order highlights the contrast:

• se non crudelem, sed clementem puts not cruel, but merciful in a prominent position

Then the infinitives come after:

• esse velle = to want to be

A more English-like order would be something like:

• Mater dicit se velle non crudelem, sed clementem esse

But the given word order is perfectly good Latin and gives strong emphasis to the contrast between crudelem and clementem.

The indirect statement is:

• Mater dicit se non crudelem, sed clementem esse velle.

In direct speech, the mother would say something like:

• Non crudelem, sed clementem esse volo. = I want to be not cruel, but merciful.

Notice the changes:

• se becomes the implied I
• velle becomes volo
• crudelem and clementem would normally become nominative if expressed with a nominative subject, but with esse volo and an understood ego, Latin often leaves the adjectives to be understood through the construction; many learners are safest thinking of the direct version mainly as:
  • volo clemens esse
  • I want to be merciful

The key point is that the indirect statement turns the mother’s I want into she says that she wants.