The doctor told my partner he has an overactive thyroid caused by him smoking didn't offer any meds but now we are ttc could this affect this?

Don't think so: Smoking causes lots of problems, but overactive thyroid is not one of them. If your partner has hyperthyroidism, the overproduction or over-release of thyroid hormone, there are many causes, including viral infections and auto-immune disease. Further testing should be done. Ask for a referral to an endocrinologist, a specially trained physician in this area.