I know that the Tyranid campaign rules aren't really set in stone, so there's no answer to this question. So, instead of an answer I'd like your opinion:
During the course of a campaign, a Tyranid Cruiser gains the Reinforced Carapace upgrade four times. The Tyranid player has a brand new Hive Ship! The campaign continues and the Hive Ship gains another Reinforced Carapace upgrade. Can the ship take it? The upgrade specifically says that it can only be taken four times.
A. Yes! When the ship received the fourth upgrade, it ceased to be the same ship and was instead replaced by another (bigger) ship. The new Hive Ship may take this upgrade up to four times again.
B. No. The upgrade says that the ship BECOMES the Hive Ship, so it's still the same ship.
Follow up question: Assume option A is correct; what happens to any other upgrades (such as Extra Spore Cysts) the Cruiser had?
C. Sorry, you can't have your cake and eat it too! If you grant that the ship becomes a new ship, and loses its four Reinforced Carapace upgrades, it loses any others too.
D. There's nothing in the description that says specifically it loses any other upgrades. In the spirit of fairness, the ship would keep other upgrades (but they would be bound by the limitations of the upgrades).
Regardless of your answers above, what is the Hive Ship armed with?
E. Whatever you want! Go nuts, as if you were buying a brand new Hive Ship. However, you'll have to upgrade its points value and pay those points if you ever want to use it.
F. If you think that the ship is the same ship, then naturally it would have the same weapons. This, of course, would leave the new Hive Ship a bit undergunned compared to a new one.
I'd say that A and C are correct, the moment the ship gains the fourth upgrade, the wording in Armada says it "matures" into a Hive Ship. To me, this says that it stops being what it was and becomes something new. Any upgrade it had is consumed, reconfigured, or rejected to grow synapse organs. As a corollary, this means I support option E. Buy whatever you want!