The first thing that comes to mind are that ninjas are most likely your primary fighters. This does not mean non-ninja soldiers don't exist, it does mean that they are likely not fighting.
Ninja Ninja Tactics
Head-on combat will be decided by skill, deception, trump cards, and a bit of luck. You need to know your opponent's strengths and weaknesses relative to your own so you can devise an appropriate strategy or counter. Sometimes that strategy really is to hit them hard and fast, while other times it is about who has the better trump card.
For what it's worth: My bet is on the giant furrball of rage for best trump card.
Group combat has the extra dimension of more combatants, but will distill to each side trying to gain incremental advantages until the other side cannot overcome the disadvantages piled against them. This can come from trying to align beneficial single battles, clustering your enemies together to bomb them with a giant fireball, or trying to gang up on one fighter at a time.
Ninja Ninja War
War is a different beast -- a many-tailed and suprisingly deep beast.
Information is vital. Not just on your terrain, but on your enemy elite. You need to know things like the lay of the land you want to invade, what defenses the towns/cites have, anything particularly special about your enemy forces. A kid turning into giant sand beast of destruction will be bad for your army's health -- good to know these things first.
This stage it is your espionage against their counter-espionage. All manners of deception are in play here, and the goal is not to be neutralized. Take that as you will. Disguises, illusions, and sometimes even being obvious in your actions all have their place in a war of information.
When it comes to actual fighting, well the civillians are ideally not to have war on their doorsteps. Or at least overt war. The best way to kill your enemies is in their sleep with a sharp kunai -- or any other way that does not involve actually fighting people and limits collateral damage to exactly what you want it to be.
Ideally, a war will end with the death of the enemy leader and not enough ninja forces thinking straight to prevent an effective immediate succession of leadership to keep fightning you. But even old leaders are wily and strong and know a lot of ways to skin a snake. Be wary of old ninjas -- they do not get there by being nice little pushovers.
Non-ninja soldiers are most likely in support roles as opposed to a raw combat role. They might even make good espionage agents if only for the fact that ninjas will be looking for ninja magic and miss things like a random person using mundane disguises. Mundane scouts can still search for information and if they are disguised enough, can be easily overlooked by faster moving aerial ninjas and still spot remnants of their passage.
As D&D Players can attest -- The True Seeing spell does nothing against a mundane hide check. A similar principle can be applied in a gambit for information.
Now nothing stops a ninja army from razing everything to the ground and just expanding on it, but really your ninja force of elites are soldiers. Many are not likely to be farmers or carpenters, or be in the trade of maintaining land. But unless there are only two powers in the world, the other powers will be paying attention and may provide help at the most inconvenient moment. Or attack your other flank while you are busy looting and pillaging.
On Stupid Kids in Orange Suits
Disposable bodies that return information to caster and the ability to look like anything are powerful skills if used right, either as an impromtu fighting force or as a disposable disguise. Giant toads might be a bit obvious, but they are effectively portable siege engines -- giant snakes are capable of doing good damage to a city. Toads jump and have weapons so that helps them.
While yelling out your technique names is bad for stealth, if you yell your clone technique in a forest and nobody hears you, did you call it out? Also he is a stupid kid with little training right now -- he will improve. Hopefully.