I think the injections block out a lot of the pain. During the first session when I was on neurontin I went from a headache every day to 3 or 4 out of 7 days, which was phenomenal for me as I've had daily migraines for at least the last year and 5 out of 7 days for the last five years.
The neurologist, however, felt he could improve on this and switched me from neurontin to topamax and I have been suffering ever since. Now, having said that, these headaches are different. They're in no way related to muscles and pretty much nothing works to relieve them. They seem to be either withdrawl from or a side effect to one of the anti-epileptic medications.
So I think the short answer is yes the Botox works, especially if your muscles are at all involved in triggering the migraines. I tend to worry a lot and grind my teeth at night. The Botox paralyzes the muscles in my forehead and so they don't tighten when my jaw does. I'm scheduled to have my third set this time and am hopeful that I will see more improvement as the reactions to the medications calm down.