Hi Johraf... Thyroid nodules are quite common and very few of them ever turn out to be cancer. Since your wife had a thyroid ultrasound, that would told the endocrinologist the characteristics of the nodule and they would have been able to tell from that, the likelihood of the nodule being cancer. Apparently, those characteristics did not indicate signs of cancer.
Sometimes, anxiety can make it difficult to swallow and it really feels like there's something stuck in the throat and feels like we're going to choke... I have quite a few nodules on my thyroid and I've had this happen before - it wasn't the nodules causing the problem; it was my anxiety, even when I didn't "feel" that anxious.
Can you tell us what other tests the doctor did? He should have ordered some blood tests, which, hopefully, would have included Free T3, Free T4 and TSH. If you can post the results of these tests, along with the reference ranges from her lab reports that would help us greatly to assess the testing/treatment that's being done. He should also have ordered antibody tests to determine if your wife has Hashimoto's Thyroiditis. Those tests would be Thyroid Peroxidase Antibodies (TPOab) and Thyroglobulin Antibodies (TgAb)... Both of them are necessary, as they are both markers for Hashimoto's and some of have one or the other, while others have them both... Nodules are very common with Hashimoto's, which is the main cause of hypothyroidism.
Levothyroxine is the main medication prescribed for hypothyroidism and it will, often, help shrink nodules. What dosage of Levothyroxine did the doctor prescribe and how long has she been on it? It does take 4-6 weeks for the levo to reach full potential in the blood and it's not unusual for symptoms to worsen or for new ones to appear, as the body adjusts to having hormones it's been doing without.