There's a world where ninjas have vast magical powers (up to creating great fireballs, small tornados or tsunamis) and unhuman level of speed and endurance. On the other hand, there's no stupid ninjas running in orange suits, shouting their techniques names so enemy knows what to expect and certainly there's no commanders stupid enough to send their army running in one big blob against second big blob of ninjas, where most of these ninjas know techniques with such big area of damage.

Also supply is much lesser problem. As ninja are scarce in population, there's less mouths to feed. You can also just seal supplies in a scrolls and send just one person which would be as effective as whole supply convoy.

So, in theory, there's not much problem with sending some good ninja deep into enemy territory to obliterate city or two and go without a scratch. When there's not many ninja and a lot of terrain, it's easier to sneak by than protect vast borders.
There's so much power difference between (even mediocre) ninja and normal human, that later stand no chance. There's manpower to send normal levy as scouts or guards, but they would be as useful as their corpses saying "there was enemy here".

I see a lot of offensive potential in armies of this world, but not much defensive.

So my question is: how could warfare between ninjas look like without it being about who strikes hard first?

I wouldn't like to go for resolution such as MAD so warfare (symmetric or asymmetric) would be viable for this world.

You can think of power limit as scaled down Naruto, without power creep that was introduced after Chunnin Exam and later.