Depth of field comparisons are rather slippery things unless the criteria used for the comparison are clear. In general, and at close distances (ie well away from the hyperfocal distance of the shorter lens), lens focal length has no effect on depth of field if the magnification, effective aperture and format are kept the same. As you approach the hyperfocal distance of the shorter lens, the shorter lens will give greater depth of field.
If you suppose that the 60 mm and the 105 mm AF Micro-Nikkors maintained their focal length, the depth of field at an effective aperture of f/11 and a magnification of 1x (ie a reproduction ratio of 1:1) is 1.3 mm for both lenses. At a magnification of 0.5x, the DoF is 4.0 mm for both lenses.* You can use one of the online calculators to find these results. As the DoF is not dependent on the focal length, it does not matter that the two lenses under consideration shorten their focal length as they focus more closely.
Best,
Helen
*Oops, I forgot to state the diameter of the circle of confusion that I used. It was 30 microns, which is typical for 35 mm.