The Botox molecule is constructed of two parts: the central core, comprising the neurotoxin, and a surrounding protein complex which is meant to protect the neurotoxin. The neurotoxin is what performs the magic of Botox. Antibodies may form to either element. Most of the concern regarding Botox antibody formation has to do with a theoretical dilution of its clinical effects. With this in mind, antibody formation has been studied. It turns out only about 0.3% of patients developed antibodies in well done clinical trials. Since lupus patients should be concerned about antibody formation this theoretically could be relevant. Fortunately, the antibodies that are formed do not trigger or exacerbate lupus. Therefore, there does not appear to be a problem for patients with lupus, never mind for people who do not have lupus. Similarly, there is no problem in regards to hypothyroidism, you will not develop this problem and if you already have it Botox should not exacerbate it.
Botox weakens muscles, but not the immune system.