All of the workable defense strategies I've read thus far assume the space bees are in a tightly packed formation. There is no particular reason for this to be the case, and since they are not idiots I am going to assume they spread themselves over the maximum volume possible. A relatively small sacrifice in delta V will result in very large fleet dispersals meaning that no nuclear weapon will be able to kill more than a single bee, and clouds of dust or sand will not be large or dense enough to materially affect the fleet during transit.
The OP says the fully fueled mass of the bees is 3141kg. Using this online calculator http://www.strout.net/info/science/delta-v/ an 80,000 ISP, and 70,000 m/s delta V suggests an unfueled mass of 2870 kg. That gives me a 7E12 joule energy. (i.e. 7 terajoule or 1.6 KT)
The total energy of the fleet will be 7E20 joules or 170,000 MT. The bolide which killed off the dinosaurs is estimated to have had 130,000,000 MT of energy, so the bees would have almost 1,000 times less energy if they all get through our defenses.
This handy calculator gives you the effects of an individual impactor. http://impact.ese.ic.ac.uk/cgi-bin/crater.cgi?dist=.001&diam=2.76&pdens=261&pdens_select=0&vel=70&theta=90&tdens=2500&tdens_select=0 projectile diameter is 2.76m, density is 261 kg/m^3, velocity is 70 km/s, angle is 90 degrees. The one problem it has is that it assumes an impactor tensile strength of a natural material, whereas these impactors are made from carbon nanotubes. I don't know how to calculate how atmospheric frictional heat loadings affect the material, nor what kinds of tensile stresses result from the atmospheric traversal, but I think it is safe to say the impactors would penetrate to a lower altitude than indicated in this calculator. 912
But since the calculator has the impactor detonating into a fireball at 121,000 meters altitude, I think it's very unlikely that it would reach a low enough altitude to markedly affect the surface before it detonated into a fireball.
The other noteworthy takewaway from this calculator is that the fireball energy is only 1/7th the kinetic energy of the impactor. (Presumably the rest is lost to friction prior to this point.)
This puts the attack in a very different light. Essentially all of the energy of a fleet attack which was well distributed across one half of the Earth would go toward heating the atmosphere, producing little or no effects on the ground other than loud noises and bright flashes of light.
In order to produce any truly dangerous effect, the attack would have to be focused. If the bees fire a dense stream of impactors at selected targets, they can produce deeper penetrations. The initial impactors would produce a partially evacuated shockwave in their wake, through which the following bees could travel with less energy lost to the atmosphere as friction, resulting in lower detonation altitudes (possibly not detonating until impacting with the surface). Also, the thermal flash effects would be concentrated in one area, resulting in arbitrarily high thermal loads in that vicinity.
Potential strategic impact sites might include the Yellowstone super volcano (possibly requiring the entire fleet to cause any likely volcanic effect here?), nuclear reactors, flash heating attacks on drought afflicted forests in order to cause massive firestorms and nuclear winter effects (nuclear winters rely entirely on sending smoke into the stratosphere via a firestorm), flash heating of crop lands in order to create famine conditions, bioweapon research labs (human diseases are pretty bad, but just as horrible would be the effects of uncontrolled release of novel crop diseases), and oil refining and storage facilities (cripples our economy and contributes smoke to stratosphere).
One problem with focused attacks is that they make it easier for the Earth to degrade the attack (with nuclear detonations in space and sand cloud attacks). The goal would be to degrade the nanotube structures to make them break up higher in the atmosphere. The higher the altitude at which the impactor breaks up in a fireball, the less the damage to the surface.
I think the bees would be smarter to invest in larger and denser but fewer impactors. Carbon nanotubes might be good material for the outer skin (I'm not sure) but the impactors should carry a payload of natural (non-explosive) uranium, tungsten, or other extremely dense material. The impactors should be shaped like arrows, not like pods. They need to lose as little energy as possible on atmospheric friction, and density is the key to this. The impactors should come in a variety of sizes. 435