I think both have their uses. I would probably never use a vampire military, because the vampires' speed seems to be affected by alcohol withdrawal, but they're awesome for a lot of tasks-- never sleeps/eats/drinks makes up for lost speed when it comes to production, and simplifies putting them in physically isolated burrows for purposes of keeping watch or doing logic. I've already experimented with vampire woodcutters and vampire weavers (both worked fine), and am thinking about experimenting a bit with vampires in the food production chain (a vampire, a kitchen, and 200 chickens in a burrow).
Werebeasts sound promising, but I understand there's a lot of difficult infecting dwarves (civil war type difficulty). If you can make all of some group of dwarves into the same kind of werebeast, then the idea is, they should all change at the same time, and then nobody gets killed, which is a nice idea, and since they don't really need to eat or drink, it's not hard to keep werebeasts isolated from your general pop, no harder than it is for vampires. But I think that once you have a legendary warrior, it would be rather more of a pain in the ass than a help if he suddenly dropped his weapons and armor and turned into a horse while charging goblins-- but then, I've never seen a legendary kicker horse, it's probably something fearsome.
I think that probably the best military application would be marksdwarves, because of the kind of injuries marksdwarves sustain, and because they're probably never in a situation to charge the enemy unarmored. You could even use cage traps on likely posts to protect any dwarves that fall unconscious, without worrying about starvation. I think a group like that could be functionally immortal, rapidly turning into legendary marksdwarf/shield user/dodgers.