Preety,
Actually the decision of taking iron pills should not be taken by the doctor unless a full iron studies are done. If these studies showed iron deficency, only in this case you will find that iron will be helping your body and will be also reflected on the hemoglobin. By taking iron in this case, you are correcting the iron deficiency anemia not the thalassemia trait.
If you didn't have iron defiecny, so these iron pills were wrong to take because they harm the body by being overloaded in the body organs (liver, heart, glands,...). Having a low hemoglobin too, adds to this problem because when the HB is low, iron is heavily absoarbed from food in the gut ( a way the body defend itself) . So you end up having iron absoarbed from the gut in addition to what is added from the pills. All this iron can be stored in the organ making them function improperly. By the way, low ferritin does not show this iron overload in organs, it is seen only in scans.
As for the hypothyroidism, i observe that a lot of minors have a hypothyroid gland, i don't know if there are any studies done on this or not (you can hardly find studies on minors anyway)
Hope this helps, please feel free to ask anything
manal