Theoretically there are two very basic things to consider in judging virulence for the secretion systems: a) Can it secrete into any human cell? (If not, chances of being virulent are smaller, but not zero as whatever is secreted in the environment of a cell could also be harmful for the cell.) b) Does it secrete some agent (protein, RNA, molecule), which is potentially harmful for a human cell?
a) alone is not sufficient for it to be virulent if b) is not also given. (As it could inject something in a cell that the cell can handle without a problem.) b) alone is not sufficient, as it has to get inside the cell somehow. Although, b) alone can work, if the agent has another way to get inside a cell or to harm the cell from outside.
So, generally, without knowing ALL the bacterial secretion systems and secreted agents, it is impossible to decide if one secretion system (alone) is always, sometimes or never harmful.