В письме было слово в скобках, и я не сразу понял, зачем оно там.

Because в письме is in the prepositional case, which is used after в when it means in or inside a place.

• в письме = in the letter
• в письмо would normally suggest motion into the letter, which does not fit here.

So this is a location, not movement:

• в письме было слово = there was a word in the letter

Было agrees with слово, which is a neuter singular noun.

• слово = word
• past tense of быть matches it:
  • был for masculine
  • была for feminine
  • было for neuter
  • были for plural

So:

• было слово = there was a word

This is a very common Russian way to introduce the existence of something:

• В письме было слово... = There was a word in the letter...

Because скобки usually means parentheses/brackets as a pair, so Russian normally uses the plural.

• скобки = parentheses / brackets
• в скобках = in parentheses / in brackets

Even if English often says in brackets or in parentheses without thinking about number, Russian treats them as a pair, so the plural is standard.

Не сразу понял means didn’t understand right away or didn’t understand at first.

• сразу = immediately / right away
• не сразу = not immediately
• понял = understood

So the idea is:

• first, the speaker saw it
• then, understanding did not happen immediately
• only later did it become clear

It is a very natural Russian expression.

Because понял is perfective, and here Russian is talking about the result or moment of understanding.

• понимал = was understanding / used to understand / understood in an ongoing sense
• понял = understood, got it, figured it out

In this sentence, the speaker means:

• I didn’t understand it right away
• in other words, the moment of understanding did not happen immediately

That is why понял is the natural choice.

Because зачем asks about purpose or what for, while почему asks about cause or why in the sense of for what reason.

• зачем оно там = what was it doing there? / what was it there for?
• почему оно там would sound more like why was it there? in a causal sense

Here the speaker is wondering about the function of the word in parentheses, not the cause of its existence. So зачем fits better.

Оно refers to слово.

That may feel a little strange in English, because English often says it without much attention to grammatical gender. In Russian, the pronoun must match the noun:

• слово is neuter
• so the pronoun is оно

It does not refer to скобках, because:

• скобках is plural
• and it is part of the phrase в скобках

So:

• зачем оно там = why/what for it was there
• where it = the word

Там literally means there, and here it means in that place.

So:

• зачем оно там = why was it there? / what was it doing there?

Even though the sentence already mentioned в скобках, Russian still very naturally uses там to refer back to that location. English can do something similar:

• There was a word in parentheses, and I didn’t immediately understand why it was there.

Because зачем оно там is a subordinate clause.

Russian normally separates subordinate clauses with commas:

• я не сразу понял, зачем оно там

Literally:

• I did not immediately understand, why it was there

In natural English, we often omit the comma, but in Russian the comma is required.

The word order is fairly flexible, but the given version is very natural.

• В письме было слово в скобках, и я не сразу понял, зачем оно там.

This order presents the information smoothly:

1. setting: in the letter
2. new item: there was a word
3. extra detail: in parentheses
4. reaction: and I didn’t understand right away...

You could change the word order, but the emphasis would shift. For example:

• В письме в скобках было слово...
  This puts more focus on the location in parentheses earlier.

So the original sentence is a normal, neutral way to say it.

Yes, sometimes в скобках can be used more loosely for something inserted parenthetically, not only actual punctuation marks. But in a sentence like this, the most natural reading is literal:

• a word in parentheses
• a word in brackets

So unless context suggests something more abstract, a learner should understand it literally here.