" a 5mm ‘cystic lesion’"
That might be very common, and benign. Just guessing, but plain cystic (i.e., uncomplicated fluid) should = benign.
"when a young male has a thyroid cyst and swollen nodes that is very suspect"
Except any metastatic nodes would be expected be likely downstream from the thyroid, which yours are not.
"Would my FNA of the one lymph node have shown thyroid cancer were it in the nodes? "
Yes. The first step is to see via microscope any cells wherein the nucleus looks deranged. Also, metastatic nodes usually have calcification which the USs would have seen.