Are you forgetting they are all magic users?
The Samurai are the Shogun's personal guards and protect him first, city second. That's about their only job. They are not traditional samurai like the japanese, but inspired by them. They wear heavy armor and two swords, and have some magical capabilities as well to help them fight even better. And think about it. Why shouldn't they be able to carry armor just because they are inspired by the Skaven? The Skaven part is just in the looks area anyway. Their armor and weapons are custom made by rats, for rats. And think about who gets to be a samurai in the first place. These are only the best of the best, the elite soldiers among the elite. Of a hundred professional soldier rats, only ten get the chance to be a samurai, and only five of them passes the tests on average. That's 5% of the best soldiers in the entire army. And even when they do become samurai, they are trained specifically by older samurai to be even better than their masters. Why can't such elite soldiers fight in armor and weapons made especially for them? Also think about the real samurai. While most of us think the katana is just a samurai sword, each sword was made for a single person. This sword became as much a part of him as his actual hand. (that's why the katana usually have names. Watch Kill Bill Volume 1, and you see how special a katana really is.)
But as for the regular soldiers and ninjas, they are like most rats. They lack in weapons and are not very strong in close combat. They depend on shadows, hiding and guirilla tactics like attacking from behind and vanishing before the enemy knows what hit them. This makes them formidable opponents, even if they are small and much weaker than their enemy. Ninjas on their hand are pure assassins and thieves, or kinda like a strike force. They get an order where to strike (for sabotage, kidnappings, assassinating someone, steling something etc) and follow the order to death. They either succeed with their mission or die. Failure is not an option. This again means they work in small numbers or clans, usually not more than five or six. Only the ninja master knows their true identity, so even a clan of five ninjas doesn't know who each other are, only what their nickname is. (as an example, Princess Sophitia is known as a noble, peaceful princess and couldn't be further from the ruthless ninja Ravenheart - even if they are the same person. Even the other ninjas in her clan doesn't know her true identity. Even her father, the Shogun, doesn't know who Ravenheart is.) This is to prevent emotions from jeopardizing the mission. Each nina considers himself or herself dead when they start a mission, so while they help each other as much as they can, no one mourns for a fallen ninja. If a ninja dies, he or she will be celebrated after the mission, and that's it. No funeral, no purple heart or anything. This again is because being a ninja is very dangerous occupation, and everyone is aware of it before they even join a ninja school.
Anyways, there you go. Don't think "skaven" as much as "looks like skaven". And for that matter, I don't even like Warhammer that much. I read a few books, but got bored quickly. Why then should I copy an entire race from Warhammer into my fantasy novel? Just because Warhammer had humanoid rats, it doesn't mean no one else can use them. And they are at least cooler than elves and dwarves.
