For aircraft the canard loses in two out of three performance categories.  The canard wins the low speed controlability since it is easy to design so that it won't stall.

Canard 1, conv 0.

This same ability also means that you can't raise the nose at slow speed like takeoff so your takeoff ground run will be longer and you'll need a longer runway.

Canard 1, conv 1.

At cruise the canard will always have a higher wing loading or be closer to its max angle of attack since it has to stall first.  This is higher drag.

Canard 1, conv 2.

Now can you make a perfectly good airplane with a canard? Of course.  I've flown the Velocity (canard); it would be hard to find something easier to fly.  It just spends more time on the ground accelerating because it needs more speed to fly.

Now for a missle you wouldn't have the slow speed regime to worry about.  You would have an extra set of fins up front, additional drag.  You could probably make it turn quicker if that's a requirement.  Ordnance is often best accomplished with the lowest cost item that does the job.  Since I've never done anything with missles you might want to ignore this last paragraph and wait for someone more knowledgeable than me to weigh in, like my dog, anybody but me.

greebling,

You will find additional information in:

 FAQ2-760,Pros & Cons of Standard, Canard, and 3-Surface Airplane Configurations

If this reference doesn't link, go to the Aircraft Engineering thread and click on the FAQ tab at the top.