A timely NIP is only required to successfully prosecute the speeding offence. If the NIP was received late (or even not at all) it does not invalidate the accompanying (or any subsequently served) s172 request.
Since the speeding offence is now irrelevant, so is the NIP and its timeliness.
I think if the recipient is deemed to be a "body corporate" you will have difficulty defending this. The very section - 172(4) - which you are relying on as a defence is not available in those circumstances (which, as I said, I am not able to comment on). In that case it is only available if the body corporate can show that no records were kept (and they obviously were not) and you can convince the court that it was reasonable not to do so.
It's a shame because you have at least the basis of a decent "reasonable diligence" defence under s172(4). It might therefore be better if you could convince the court that the recipient of the s172 request was an individual. Then a defence under s172(4) would be available to that individual unconditionally. But, from your description of the arrangements, I'm not quite sure how that could be done.
Meanwhile, in case you need to demonstrate it to the court, what are the circumstances surrounding this vehicle and the people who may drive it which might make the requirement to keep records of who does so unreasonable?
Moving a little further along, if "the trust" did end up convicted and, as southpaw suggests in post#2, it has no "legal identity", I'm not sure how any financial penalties imposed might be enforced. But once again, not something I have enough knowledge of.