I have an underactive Thyroid and am on Thyroxine as well and recently took my Class 1 and passed. I told the CAA all about it and put it on the form plus spoke to them by phone about it. As long as your Thyroid level is stable and you have no ill-effects they don't seem to have a problem with it.
The main problem it has caused for me is a tendency to put on weight!
Desk Pilot