Штраф за просрочку и страховой депозит указаны в договоре хранения.

Because the subject is actually two things joined by и:

• штраф
• страховой депозит

Together they form a plural subject, so the predicate must also be plural:

• Штраф ... и страховой депозит указаны ...
• The penalty ... and the security deposit are specified ...

If there were only one item, you would use singular, for example:

• Штраф указан в договоре.

Указаны is the short passive participle plural form of указать.

In this sentence, it means something like:

• are specified
• are stated
• are indicated

This is a very common formal written style in Russian, especially in contracts, rules, and official documents.

Compare:

• указан — masculine singular
• указана — feminine singular
• указано — neuter singular
• указаны — plural

Here за means for, and it takes the accusative case.

So:

• просрочка → nominative
• просрочку → accusative

The phrase штраф за просрочку means a penalty for delay / lateness / overdue performance.

This pattern is very common:

• плата за хранение — payment for storage
• штраф за нарушение — penalty for a violation
• ответственность за ущерб — responsibility for damage

In legal or business Russian, просрочка usually means a delay past the required deadline: something is overdue or late.

Depending on context, it can refer to things like:

• late payment
• late pickup
• overdue performance of an obligation

In a storage-contract context, штраф за просрочку often means a penalty if something is not done on time, such as not collecting stored items by the agreed date.

В договоре is prepositional singular after в, meaning in the contract.

But хранения is genitive singular because it depends on договор:

• договор чего? — хранения

So literally this is:

• in the contract of storage

Natural English would usually be:

• in the storage contract
• in the storage agreement

This is a very common Russian structure: one noun modifies another by using the genitive.

Literally, it means contract of storage.

Grammatically:

• договор = contract, agreement
• хранения = of storage, of safekeeping

Russian often uses a noun + genitive noun structure where English might prefer an adjective or compound noun.

Examples:

• договор аренды — rental agreement
• договор купли-продажи — purchase and sale agreement
• договор хранения — storage agreement

So хранения is not describing договор as an adjective would; it is a noun in the genitive showing what type of contract it is.

Страховой is an adjective modifying депозит.

It agrees with депозит in:

• gender: masculine
• number: singular
• case: nominative

So:

• страховой
  • депозит

In context, this usually means something like:

• security deposit
• insurance deposit
  depending on the exact legal meaning in the document

The adjective comes from страхование / страховой, related to insurance or financial protection.

Russian usually does not use a present-tense equivalent of to be the way English does.

So instead of saying something literally like Penalty and deposit are specified, Russian often just uses the participle as the predicate:

• Штраф ... и страховой депозит указаны ...

That already means are specified.

This is normal Russian style, especially in formal writing.

Yes. Russian word order is more flexible than English word order because case endings show the grammatical relationships.

For example, these are all possible:

• Штраф за просрочку и страховой депозит указаны в договоре хранения.
• В договоре хранения указаны штраф за просрочку и страховой депозит.

The second version may sound a bit more natural if the speaker wants to emphasize where the information is given: In the storage contract, the penalty for delay and the security deposit are specified.

So the original sentence is correct, but it is not the only possible order.

Russian has no articles.

So nouns like штраф, депозит, and договор do not automatically show whether they mean:

• a penalty / the penalty
• a deposit / the deposit
• a contract / the contract

You understand that from context.

In this sentence, because it sounds like a specific formal document, English usually uses the:

• The penalty for delay and the security deposit are specified in the storage contract.

Not in this sentence, if штраф and страховой депозит are the subject.

Since there are two coordinated nouns, plural указаны is the normal and correct form.

• Штраф и депозит указаны ... — correct
• Штраф и депозит указано ... — not standard here

You would use указано with a neuter singular subject, or with an impersonal construction, for example:

• В договоре указано, что... — The contract states that...

That is a different structure: here указано does not agree with two nouns; it introduces a whole clause.

In Russian, a short passive participle like указаны often expresses a present state resulting from an earlier action.

So in practice, here it means:

• are specified
• are stated

not necessarily were specified in a simple past sense.

The idea is: the contract already contains this information, and now, as a result, these items are listed there.

This is why such forms are very common in formal and legal Russian.