I had a lot of the same questions initially about nids instantly depopulating my ships.
The mechanic/trigger is not particularly apparent, and it was very frustrating to instantly having all of my ships reduced to drifting hulks. I wasnt sure what the cause was or how to counterplay and at first i thought it was OP as well. So i definitely can understand your concerns - new players will absolutely find this very frustrating and i think transparency could be improved so that at least you have a better understanding of what is happening to your ships. Especially because troops/assault has been significantly reworked from the first game.
I then made a post on the forum trying to get more information on assaults (ashardalon provided a very illuminating post so thanks for that!) - it made a lot more sense as far as what was happening, but still seemed very strong.
I then tried playing some games as carrier nids. When i played vs newbies with just a few battleships, i was amazed as i hulked them all instantly (they were isolated and in lock on stance) and my inital thoughts of "OP" seemed vindicated. However, then i played vs some more experienced players and really saw the limitations/counterplay first hand. This really made me realize the limitations of assault craft, and how "all or nothing" it truly is.
These more experienced players grouped up their ships, and used manuevers to make my assault boats chase them for long distances. With "brace for impact" on, these chases shot down almost all of my craft, significantly lessening their impact. When i was able to land an assault, they had LC's nearby to instantly repopulate them via lightnighy strike. I then tried boarding to rehulk their ships, but they just zipped another LC by to repopulate again... very frustrating to play against that as nids, since there seems to be no additional damage that you inflict with additional hulkings.
Assault craft seem very OP for newer players due to unclear mechanics and high baseline damage. At low levels of play they seem to overperform.
Correct counterplay seems to punish assault craft too hard at the moment. With brace, interceptors, limited charges, and minimal punishment for recrewing a hulk, assault craft are near-useless and not worth it at a higher level of play.