Are you going to add phasers like the aquashuttle had in TAS?
I've been thinking about that. Traditionally shuttlecraft throughout Trek haven't been shown with armament with exception of the DS9 runabouts. And the aquashutle is pretty much solely a research vehicle...but we did see it with phasers. I think we could rationalize that shuttlecraft usually aren't armed, but that perhaps they can be fitted with phasers for specific missions or that some shuttlecraft are equipped with armament for specialized assignments where there may be a higher possibility of risk to the craft and personnel.
I would think the Class F shuttlecraft wouldn't be armed since they are strictly transports and science reconnaissance craft. The heavy lander is also a purely scientific research vehicle so I doubt there would much need for it to be armed. Of course both of these craft might utilize phasers for other reasons than defense or combat. I think the scoutship could be fitted with phasers because although it's primarily a fast transport it could also be used for limited covert missions and reconnaissance, situations where some defensive armament, even if limited, could be welcome. And since the aquashuttle is meant to go into unknown environments where something could conceivably threaten it then some weaponry could be useful.
The bigger question in my mind isn't whether the aquashuttle could be armed, but how are energy weapons supposed to work under water anyway???