Those stats are working fine, but the problem is in how they are calculated in and in how, resistance/defense modify the damage suffered by a target.
With our current damage formula (look at a stacking ninja like kimimaro), the higher the def/res the more close to 100 will be the damage landed by the enemy, so, very likely is a decreasing exponential. The issue is that the quantity of defense/resistance stacked on ninjas by equipment and basic stats right now is way lower than the quantity of atk/ninjutsu and to get a significative change in the number you see you have to add hundreds and hundreds of it, so, just now the effect of these two defensive stats is relatively poor, overall because many mysteries and standard attacks are half taijutsu half ninjutsu, so, unless you have both the defensive stats high you are going to suffer a big damage because is way easier to have both the damaging stats high than the defensive ones.
What do nin and tai *ion do?
They let you ignore a part of the enemy resistance and defense. Very likely the quantity stacked. So if you have 1000 nin *ion for you is like if your enemy have 1000 less resistance. The point is how big is this effect if your enemy have instead of 9000 resistance 8000 on an effect that only for half of his damage is ninjutsu based? For what we can see is an effect lower than the rng range of the damage, so, you don't even figure is there.
So, since is a decreasing exponential, you see a significative effect, if you have 1000 nin *ion only on people that have 1000-2000 resistance, but the point is that those people are so way weaker than you that you can't care less if you nuke them with a 13k blast or with a 9k, they die regardless in round1.
Could be the effect of those two stats will be less marginal when they change the damage formula to make resistance and defense more relevant,but so far this is how the things are.