Despite what you might see a lot in the media lately the EU is not a military alliance and has explicitly no involvement in the military. So joining the EU is irrelevant on these issues.
The article mentions that sovereignty is a big issue. It should be because joining the EU means giving that up so that, I think, is the really crucial issue they should be thinking long and hard about (including, indeed, with respect to fisheries).
EU is indeed a military alliance. They are just no integrated command structures but this is common among most military alliances across the world.
SAFE credits are an EU military thing.
Sovereignty is not a binary thing. And it's also not the case that not being a part of some structure makes you sovereign from it. In some cases it's the opposite - you need to conform anyway and have no input into the decision process. So as usual things are nuanced and not black and white.