>Will the bubonic plague have secondary outbreaks in succeeding decades, separate from the Black Plague situation?

After the situation ends, there might be other outbreaks of the Bubonic Plague, which might be more or less deadly depending on the resistance of the pops:

By the way, we're doing a Play & Fix session at the studio, so as I'm replying here, I keep playing - and the Plague is back!:

The Black Death has finally ended in 1354, and around 95M pops have died: