This possibility persists as long as we do not have a comprehensive briefing on gene function! For example, the transportable elements are a clear evidence to the kinetics genome!
It would probably depend on targeting efficiency and specificity of your viral vector. As most gene therapies are given into the blood stream or injected in close proximity to the targeted organ or tissues, off-target effects are reported in the liver. To my knowledge off-target effects are not known, or have not been investigated, in the reproductive system.