To elaborate on and combine a few other answers, consider that the Earth's magnetic north is not in a constant position, so it is not the factor in how lat/long coordinates are determined. Rather it is the axis of rotation as has been pointed out by others.
The equator is determined by being the great circle (circle which circumscribes the geoid of the planet), upon which twice per year (on the equinoxes) the sun travels exactly 180 degrees from horizon to horizon in a perpendicular fashion. Leap years are a thing because there is a slight difference in the time it takes for the earth to complete a single orbit of the sun vs. the period in which two equinoxes occur.
In your case a similar equator could be determined by observing the relationship between the body which the astroid orbits vs any 'wobble' along its axis of rotation (although this may take longer than a single 'year' or orbital period about the body.) The 2 points at which any two lines that are perpendicular to that equator intersect are its 'poles'. Lines which then intersect at a 90 degree angle at the poles can be used as meridians, the points at which those meridians intersect the equator are effectively arbitrary (the prime meridian is Euro-centric due to the fact that European cartographers defined it, not for any special geometric reason.)
The last step is then determined by math which describes projecting the surface of the asteroid to the abstract sphere that these lines define, surveying specific landmarks (natural or artificially placed) to act as well-known points which can be surveyed against as a reference system for any other point on the surface, allowing you to triangulate coordinates. 204
These landmarks need to be offset along either the x or y axis from one another.
On a personal note I am also a fan of the answer which mentions 'geohashing' for modern cartographical applications. I have worked on an abstract specification known as 'Discrete Global Grid Systems' with the Open Geospatial Consortium which is conceptually similar and I'd encourage you to look into it if this sort of thing interests you. Its basis divides the sphere defined by an equator and meridians into a grid of triangles which is then projected to the surface of the body. Ironically, this is shown in the illustration of the robot in the left sidebar of this site. However your question specifically mentions coordinates, which a hashed addressing system does not provide. 441