I asked this question to Rabbi Mordechai Kornfeld, the rosh kollel of iyun hadaf in harnof http://dafyomi.co.il
he replied: "There is a difference of opinion among the Torah authorities as to whether this section should be studied by the typical student of the Torah. Many Torah luminaries maintain that one should not seek philosophical proofs of G-d's existence. Belief in Hash-m should be based on the Mesorah (tradition) that we received from our elders and mentors, the study of Hash-m's wondrous Torah, and the many ways He manifests Himself in His creations and in our daily lives."
UPDATE:
(after more study of the shaar yichud)
ray: The reason the shaar yichud is so difficult is because the author tries to explain logically why we exist. ultimately this involves trying to understand that which is Eternal, and the Eternal is beyond the grasp of human logic, since it is beyond our cause/effect way of understanding things. the shaar yichud itself concludes that it is better to stay away from logical inquiry and to try to know God through His deeds as written in ch.10:
Therefore, you should exert your mind until you know the Creator through the evidences of His works and not strive to know Him in His glorious essence. For He is exceedingly close to you from the side of His deeds but infinitely remote in any representation of His essence or comparison with it. As already stated, we will never be able to find Him in this way. When you arrive at the stage where you abandon (trying to find Him) through your thoughts and senses because He cannot be grasped in this way, and you instead find Him in the evidence of His deeds, as though He were inseparable from you - this is the pinnacle of knowledge of Him which the prophet exhorts us on.
ANOTHER UPDATE:
from Rabbi Mattityahu Solomon's recently published commentary to chovos halevavos (gate 2):
"The custom practiced in the yeshiva world is not to study the Shaar Yichud. And even though, there is no doubt whatsoever that all of what he says there is absolute truth, nevertheless, his words are of philosophical inquiry and this inherently leads to many questions in the mind of the person studying them, and not every person is capable of fully understanding them. It is possible therefore that one could remain with unresolved questions, or at least with doubts, that would not have occured to him had he not studied this work. Therefore, it is customary to walk simply and accept as a given, simple faith that the Creator is One. And the explanation of One is that there is no power in the world besides Him, no place in the world devoid of Him, and nothing in the world without Him. These things are above the powers of our minds to grasp.