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Change is an ergative verb:

1. As an intransitive verb, its subject undergoes the change:

The English language has changed over time.

2. As a transitive verb, its object undergoes the change:

Someone has changed the English language over time.

Now we have someone causing the change.

3. And when you passivize the transitive version, you end up with your been sentence:

The English language have been changed over time by someone.

We still have someone causing the change, but the by someone phrase has been omitted.

So although both sentences work, the been sentence implies that it's been changed by someone. And that's not really how language change works, so the sentence isn't really true—though it is perfectly grammatical.

You also ask about three sentences:

1. How the English language has been changed over time?
2. How has the English language been changed over time?
3. How has the English language changed over time?

We've already covered the difference between sentences 2 and 3, so I'll just talk about sentence 1. This sentence has the form of an interrogative clause, but main clause interrogatives are usually marked by Subject-Auxiliary Inversion. This isn't, so it doesn't work as a complete sentence (except as perhaps an echo question or the like):

how [the English language]_subj has_aux been changed over time

It does work as a subordinate interrogative clause:

I wonder [how [the English language]_subj has_aux been changed over time].

It works as a complete sentence if we invert the subject and auxiliary. If we do that, we end up with sentence 2, which is perfectly grammatical:

How has_aux [the English language]_subj been changed over time?

This is fine.