Yes, for most folks that take migraine drugs prophylactically, they do take them for years at a time. Many women (who are 2/3 of migraine sufferers) can stop after menopause though.
There are no migraine prophylactic drugs that weren't originally designed and approved for a completely different indication (e.g. beta blockers and calcium channel blockers are cardiac drugs, amitriptyline is an old tricyclic antidepressant, Topamax and Zonegran are anti-epileptics, etc.) All these drugs are intended for chronic use.