It's an unanswerable question in an objective sense, but I think it's unanswerable for reasons other that what you might have thought.
If an astral form is not materialized, that is it's purely on the astral plane, clearly Neijia will work. Assuming you can somehow SEE the astral form! Perhaps it's manifested, or you've got a handy Astral Window spell in effect (see Street Wyrd!)
The crux of the question of "Does Neijia allow you to ignore ItNW" is also centered on "does a spirit become dual natured when Materialized, or does its astral form wholly transfer over to the physical plane".
If the materialized spirit ceases to have an astral form on the astral plane, then there's nothing for Neijia to hit, and the core question is a non sequitur.
If the materialized spirit is dual natured, then Neijia is still hitting the astral form. But ItNW isn't gained on a 'per plane' basis.. the whole critter has it or doesn't have it. Striking the astral form while the critter didn't have ItNW clearly would have worked.. but while the astral form has ItNW then the question becomes is Neijia a magical attack. All Neijia description appears to say is your regular, mundane unarmed attack can hit an astral target. So, pedantically, while the spirit has ItNW it appears to me that it'll laugh off a nonmagical unarmed attack, no matter which plane it lands on.
At any rate, it's absolutely on the short list of Firing Squad errata to get sorted out more clearly. If the writers' intent was that it bypass ItNW then it will clearly say so. Speaking personally, I'm not sure it WAS the intent that you can pay some karma to bypass ItNW. In the meanwhile, my personal opinion is it's "No, Neijia will not harm a materialized spirit" but the reason WHY it's a No is unclear on which rationale is preventing it. Certainly if your group/table prefers that it does, then just imagine that Neijia counts as a magical attack and then you CAN use it. Assuming materialization does in fact leave an astral form to hit in the first place!