As far as research ships go, it's hard to imagine a period warship being much use without a new-construction deckhouse for labs, equipment, etc.
There is much space from former ammo stores und below the flight deck.
...or any conceivable reason why it would have armaments.
The ship was given to the institute under the rule it could go back into active service any time. So the fore arms were kept. And who knows what heavy armed monsters are lurking at the unknown areas of the world? Better safe than sorry.