"Unfortunately, the tool has not been published and, therefore, it can not be evaluated in this thesis." would be better.

Yes, it is correct Also, Unfortunately, the tool has not been published (YET) and THEREFORE it can not be evaluated in this thesis.

It's not incorrect, and you can find native examples with that placement. To me, the sentence would read more smoothly like this: "Unfortunately, the tool has not been published and therefore cannot be evaluated in this thesis." (Note that I removed "it" as well - the subject hasn't changed.)