I've found that a great way to honor up shinobi is to keep them in a large group and foment insurrection in provinces recently conquered by a clan not native to the province. Each time they create a rebellion they all gain honor. It takes a few successes to reach level six, but not as many as one might think. This is a great way to keep the Oda in check early on as they try to subdue the rebels in their territory while at the same time building up a large and skilled "intel/counter-intel" force.

If I decide to build emissaries at Kazusa for the +1 honor bonus (which I almost always do eventually), I also build a port for quick deployment, and a Border Fort. In this case I'll usually build the BF before training any emissaries. AI ninja just love inactive emissaries, and if you don't have the BF in place first, you end up losing a lot of them before they raise their honor up enough to have a good chance of surviving a ninja attack. Kazusa becomes an excellent ninja trap.

Sometimes a ninja will get through and make a kill in Kazusa, despite the BF. If this happens, I move any emissaries there back and forth between provinces with Border Forts or shinobi until they catch the infiltrator. I do this when I think a general is being targeted too--retreat him through provinces with counterspies, hoping any ninja will get aced before catching up with him.