The fleet ship module reduction is currently only applicable if the previously purchased zen store ship is a vice admiral/lieutenant general vessel. In those instances, you will only need one fleet ship module, as opposed to the standard four.
There is no discount of any kind for other vessels. So even if you have purchased the Rhode Island Refit from the zen store, no discount will be offered towards the retrofit or fleet retrofit.
To obtain the discount on any fleet ship, you need to have purchased (read: not used the free vet token) the Tier 5 retrofit/refit version of that ship from the C-store.
Since there is no T5 C-store retrofit of the Nova, just a T2 Refit (Rhode Island), you cannot get a discount on the Fleet Nova. There is however a Retrofit Nova which is available for 200,000 fleet credits and does not cost any modules.