I presume OP is actually talking about fleet carriers and not megaships.
My feelings on this is they will not be destroyable, so modes don't matter. No group, no matter how big, could really provide 24x7 protection of their carrier across all platforms and instances, even if it was open only.
The only option would be to provide them with significant NPC defenses so they can protect themselves.
They may be like megaships where you can harvest them for stuff, but then, that might be a tad exploitable, so again, would need NPC defenses.
I'm going to guess that they will be like movable stations, where only squadron members can dock and use the services.
If they could be attacked, then you can guarantee there would be certain player groups going around destroying other group's carriers with pretty much impunity, even it was Open only.
Do people really want to have to sit babysitting a carrier all the time on the chance of an attack? An attack which when it comes would probably involve overwhelming force as they attackers would be able to choose the time and gather all their members, while the defenders might not even have any players online at the time of attack.... and who wants to sit waiting for one anyway?