We have no idea how they could be traveling through space. They could be using something like the alcubierre drive which wouldn't be affecting by dust or micros

We have no idea how they could be traveling through space. They could be using something like the alcubierre drive which wouldn't be affecting by dust or microscopic things in space puncturing the craft, they'd just get warped around the craft with the rest of space. Plus, space is so vast and lightspeed is so slow, I can't imagine plotting a trajectory to avoid stars/planets would be at all difficult for a society so advanced.