Black holes in Universe Sandbox are like all other bodies. The only difference is that their density is set so that light cannot escape from its surface. This results in the size of bodies being much more compact, and thus much
harder to hit. The objects which pass close by will probably be slingshot away, and this doesn't have to be because the time step is too high.
Universe Sandbox doesn't make the colission with black holes any different than other bodies in the simulation, either. If the combine mode is selected, they will combine (like what I think you're imagining should happen), if bounch mode is enabled they will simply bounch off each other.
In reality, gravity is a force caused by mass, and it doesn't matter whether the mass is a black hole, star or planet. The gravity is dependent on how big the mass is and how far away from it you are. If you turn a star into a black hole, with the same mass, it will not have any effect on any orbits. But because the black hole is much smaller, if a body gets within what would've been the surface of the old star, the gravitational force on that body will be bigger, eventually reaching the point where light can't escape if it gets as close as the surface of the black hole.
I hope what I wrote is correct and useful.