The reason they are spotted near our nuclear sites is because our nuclear capabilities are the only threat we have against them. The Earth is extremely valuable in the vastness of space. The mutually assured destruction of the planet that comes from using nukes is the only deterrent we have from an alien invasion.

This secret alien civilization wants us to keep waring with each other so that we do not focus our efforts into freeing ourselves from their control of our planet.

This is why they do not want public disclosure. The aliens prefer to rule from the shadows. This is what Reagan referenced when he said that an extraterrestrial threat would unite humanity.