You can test it quite easily that it works as i said.

Put a 13k resistance lightning main with RoW in front of a Water main with less than 20k ninjutsu and use shark bomb on it.

Only use a water main alone and do not use water enhancement or nature energy gathering.

Try it with and without ninjutsu *ion (adding or removing one gold or red inner gates runes is enough).

You will see how big the difference is in the average damage you land.

The general problem is that the average nin/atk you own is higher than the average def/res the enemy owns and the buffs to atk/nin are way bigger than the buffs to def/res.

On comparable power the *ions almost never come in effect.

An example?

Lets say you run the common shisui madara itachi anbu lightning main lineup and your enemy runs the common edo hiruzen, sasori edo tensei, shisui lineup.

On par power, generally, if the enemy hiruzen owns 20k ninjutsu your shisui is around 14k resistance.

But with the buffs in play your shisui goes to 28k resistance, but your enemy hiruzen hits 48k ninjutsu. You wouldn't see ninjutsu *ion coming in place neither if there was only hiruzen buff alone in effect, but you wiould see it if for any reason he didn't use mystery in round 1, you chaos him (removing so all his buffs), sasori uses mystery to remove chaos and you use hirzuen mystery. Hiruzen now would be at 20k ninjutsu for real and in this case his *ion would apply, reducing your resistance according, down to, at most, 20k.