Hmmm, to me, it sounds as though only the second one is correct:
The speaker is apparently talking about a task that includes the "Abbildung" of "vorhandene Rechtestruktur". He and his team were not aware of this and didn't include the latter. The fact that he uses "muss" here implies that the task always includes the "AofvR" :)
Another possible sentence would have been:
Wir wussten nicht, dass die vorhandene Rechtestruktur auch hätte
abgebildet werden müssen.
This restricts his statement to the particular instance where his team failed to include that thing - i.e. it was required in this particular instance (it may still be a standard requirement, but not necessarily)
Imo this is the correct version of your example no 1 (which I can picture in a casual conversation)
No 3 doesn't really make sense, as far as I can see.