were you different factions?  see. superweapons need both their research, and labs inorder to work.

if you were same factions, I would expect a captured novalith to work. (assuming you had proper labs)

Since the rebel and loyalists have different researchs for their novaliths, cross-faction captured novas dont have the 'research' researched.

Its kinda like how if you capture a enemy subverter.  You can use the shield break, but since you dnt have researched the research for disable field, you cant use that ability... even though the player you nabbed it from was totally disabling your advent fleet with it.

Yarlen stated a while back that yes. the Cap-ship was not supposed to be able to capture structures only demo them.  Structures being captured were also causing issues with ownership of an area.  He said this would be fixed in an upcoming patch.

what is the difference between the demolishing thing and just regular laser fire? more damage taken to the building?

Hmmm. I was playing at the Rebels, and had captured a Loyalist cannon. I'll replay the scenario with both of us as Loyalists.

Eh. I wish they wouldn't take away the capturing of structures. I, for one, wish they'd still let me use it- I think the capture ability, namely when used on targets that you either haven't researched yet, or will never be able to build, is awesome. Even if, in a situation like as was mentioned with the Advent by Mr. Haze, it isn't as useful to you as it was to it's owner, it's still a unique prize, and trying to specifically capture units that are particularly strong in one faction (for instance, capturing Advent carriers) to make up for your own weakness is a really cool twist. 

All in all, I know their are complications. But I think it's not worth over thinking. I say either just let you use what you capture as is- the way it was upgraded by the enemy, with the abilities they were able to use with it, or wait until you researched them yourself, or your race's equivalent. Whatever, it doesn't really matter much how you do it I think. Personally, I'd say that you should be able to use units you capture from other races just like you would the derelict ships from 7DS- they can use their basic weapons, but no abilities, and no passive repair. But, I digress. the Novalith cannon not being able to fire is ridiculous. I'd make an exception for a situation where something is only useful for it's abilities- colony ships, repair ships, and so forth. In anyways, the Novalith cannon research is to build it, not figure out how to use it(for that matter, it STILL didn't work even after researching it). If I capture one I should still be able to use it, just like how I captured ships that I can't build yet.

EDIT: I can see why they'd take away the capturing of structures, but I object. I hope someone makes a mod where this stays in the game.

Its pretty lame that the ship won't be able to capture structures, I was so hoping to use this to counter early titan production.  Knowing that this will be nerfed later on will mean that I probably never build this ship at the start of the game.