Guide me through this as I am not familiar with Nigerian govt. issued ID. The NIN card, it's available on both physical and digital form?
Yes, it's available on both digital and physical and both are generally accepted as the official ID Card for online KYC verifications.
And the physical ones look like this one below [I grabbed them from the internet, I don't think I doxxed the person as such info and image is readily available, but... just in case, I covered some details]

Yes, that's a sample of our Nigerian NIN ID Card, and the Cards are of two types, namely the Digital NIN Slip Card and the one you just gave above, of which other samples can be found below which I got from Google.
If they give you another chance to perform KYC, may I suggest you to take the picture of your ID on a very contrast background, like a black fabric, preferrably with the edge of the card visible to highlight that it is a physical card and not a piece of print-out. If they allow it, you can perhaps show your hands holding it, pinched by the edge with your fingers
Okay, so in regards to this, here below is a picture of myself holding the ID Card as requested by you, but due to privacy I decided to cover my face and other parts of the document for security reason best known to me

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May I suggest a video verification where your security team have a video call with OP, and he can show himself holding his card, to show that it is indeed a card, which the photo on the ID matched with the face of the caller? It should leave little to no room for any more doubt.
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I don't mind undergoing a video verification in other to proof that the documents I provided were all legits, but only if Sherbet will buy into your idea