Next time you are in/with the van, check the glove box for anything from the lease company, any text at the bottom of the number plates and any stickers on the windows.
Not as definitive as the V5C, but might give an early heads-up.
If the V5C does materialise, what you need to check is that the details (particularly the address) are correct and current, and the issue date. The issue date can be found at the bottom of page 2, after the Doc.Ref.No. Alternatively, the date the latest V5C was issued can be found on the DVLA's website if you perform a vehicle check. If the V5C was issued after the offence date, then chances are the original NIP went elsewhere. If it was issued before your company got the vehicle, that's pretty much conclusive that your boss won't be showing you a V5C with their name and address on.
As regards whether you have a viable defence - you said it was a lease van, the timing of the NIP is consistent with that, and what your company said is inconsistent with the other two, Unless and until this V5C materialises, the answer is a flat no (on the "late NIP" front at least).