It\'s usually popular to work with polygons with their vertices sorted CW or CCW in vectors(2*1 or 1*2 matrices). However, how to state polygons with holes in vectors?
As others have mentioned, a polygon with holes can be represented as an exterior boundary, plus zero or more interior boundaries, all of which are mutually nonoverlapping*. If you use nonzero winding number to determine inside/outside, be sure to specify your interior boundaries in the opposite direction as the exterior boundaries (counterclockwise for exterior and clockwise for interior, or vice-versa) so that the contour integrals are zero inside the holes.
FYI, tis kind of definition/representation has been formalized in the OpenGIS Simple Features Specification (PDF).
As far as representation:
I'd probably have a cell array of K Nx2 matrices, where the first element in the cell array is the exterior boundary, and the remaining elements (if any) in the cell array are the interior boundaries. I would use a cell array because there may not be the same number of points on each boundary.
*nonoverlapping = except at individual points, e.g. a diamond inside a square:
