"The way in which knowledge progresses and especially our scientific knowledge is by unjustified and unjustifiable anticipations, by guesses, by tentative solutions to our problems, by conjectures"
Science proceeds on a faithful belief that there is order to nature, and on that basis seeks to explain natural phenomena as best as possible. If for not faith, science could not proceed accordingly.
What Popper is getting at is that before science can test
anything, we must hypothesize. If he's saying that faith is needed in an underlying order to the universe, then it is an axiomatic faith that we must all have in order to survive. The same faith we have that if we tie our shoe with one method, that same method will work next time. That is a faith that transcends science; it affects every human. It is a simple faith, a trust in the uniformity of nature.
Theists believe in a god that is the prime source of all creation. They've imagined this, they've "guessed" this is true based on claims of revelation AND faith of things unseen.
That is a complex faith, entailing many consequences about the way the world works, and is not necessary to function. We do not NEED this faith to survive. The primary distinction here is that the simple faith of scientists can be affirmed on a daily basis. The faith of the religious can not be affirmed in the same way.
On one hand(science), we have conjectures that can be thrown out if they are shown to be false. On the other hand(religion), we have conjectures that cannot be shown to be false. That is a categorical distinction, and the most important distinction between science and religion. Because unless we have a criteria for demarcating the true from the false, we will never know what is true and what is false.
This distinction is the key to understanding why scientific knowledge has exponentially expanded. Untrue conjectures are discarded by the thousands, and the vast minority that are left over are considered provisionally true. Religion has no such method to filter out the true from the untrue. The only "progress" religion makes is a mile-high scaffolding of further speculation and interpretation which can never be resolved.
This lofty goal science has to obtain a theory of everything is fantasy. Almost to the point of believing in a fictional Never-Neverland. The quest for the whole truth is impossible for it would require one to know everything about everything. But the quest often turns to the desire to know something about everything, and then everything about something. Nothing like this is realizable.
There are many aspects of life where we set our ideals to an unachievably high level. Are you saying we should lower our goals? Would setting such a limit ensure that science progressed faster? It would not. I constantly speak of my unachievable ideals, with the understanding that it doesn't indicate a "goal", but a "direction". We must make progress, and setting goals along the vector of an unachievable ideal is a good thing, not a bad thing. The limiters are removed, and we maintain open minds.
How should we deal with the metaphysical nature of this area of science?
Shall we give our blessing to it despite its non empiracle nature?
The same way we've done it since Aristotle. Through the philosophy of science. Popper was a philosopher of science, and made great progress in that field. The questions you pose are for philosophy, not for science.
I think you mistakenly believe that science is encroaching upon philosophy. There is a well understood distinction, and conversations about each have their jurisdiction. Posing philosophical conundrums as a weakness of science is a failure to realize that science does not answer them; the philosophy of science answers them.
In other words, you're straw-manning science. Even if scientists make this same mistake, you should realize their error, instead of making it yourself.