I had my septate removed this past June. Day surgery and some minor cramping. It was totally worth it - much higher risk of miscarriage with septate. Good luck!
I have PCOS also and there was speculation of an underdeveloped uterus as well. According to my obgyn, you are still able to conceive but, of course, it will be more difficult. Medicine injections can help with the PCOS. When it comes to the uterus, you may have to be on bed rest once you are pregnant and there may be more complications for you but it really depends on person to person. At least that is what she has told me. But all doctors are different.
There is a surgery that you can get to remove the septum. I'm surprised your doctor hasn't mentioned it, possibly he thinks that with polycystic ovaries you will have other issues trying to conceive.