Detonating a few meters underground gives you a much better coupling factor. Coupling factor is the percentage of energy from the blast that is turned into ground shock/cratering effects, versus the amount that turns into air blast/surface effects. Since ground shock is the primary kill mechanism against buried targets, and the difference can be a factor of ten or more, it's a nice add-on if you're targeting silos, and it's a massive improvement if you're targeting bunkers.
The main potential downside I can see, aside from making sure the bomb survives the impact, is the weight of the earth-penetrating casing. I'm not sure how much that is, but if it's very heavy, I can certainly see SAC deciding that the extra utility just isn't worth the lower number of MIRVs.