Change is a labile verb, meaning that alongside its transitive use there is an intransitive use in which the transitive object becomes the subject. This latter use is sometimes called middle voice:
As an intransitive verb, its subject undergoes the change:
The English language has changed over time.
As a transitive verb, its object undergoes the change:
Someone has changed the English language over time.
Now we have someone causing the change.
And when you passivize the transitive version, you end up with your been sentence:
The English language have been changed over time
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. (Or something—see Esoteric's comment below.) And although this is perfectly grammatical, it may or may not be what you want to say.
You also ask about three sentences:
- How the English language has been changed over time?
- How has the English language been changed over time?
- 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 hasaux been changed over time
It does work as a subordinate interrogative clause:
I wonder [how [the English language]subj hasaux 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 hasaux [the English language]subj been changed over time?
Though note, as previously discussed, that this question implies it's been changed by someone, which, depending on context, may not entirely make sense.