The use of the word 'have' in the first sentence makes the statement sound past tense, or like it has happened already. While the second sentence sounds like you are saying that it will take a lot of time to understand, meaning you have not started to understand the hypothesis.
Another thing is that the first sentence can be kind of confusing. The word 'It'll' or 'It will' is used to say something that will happen in the future. While understood is used to talk about how you understand something already, so the two used in the same sentence doesn't always make sense.