This is an idea for drilling holes straight, through irregular shaped objects. ( I am using one if my raven whistles as an example here.
Lining up the holes when you are drilling from both sides of a bead can be a challenge. My solution is to drill one side part way and stick a pin in the hole. This allows me to see exactly where the hole is on the first side when I start the hole on the other side. When the two holes get close to the centre of the object, the pin falls out and the two holes match up..