Look at the shark that it comes with. Does it believe this submarine is also a shark, perhaps a godshark? Were the Aquasharks able to train sharks to do their bidding, to domesticate them?
Why were the Aquasharks and Aquanauts eternally fighting for the chrome crystals. Were they a power source? Crystals according to both Rock Raider and Power Miner (two similar themes from different generations) mythos were a source of power. The Mars Mission theme also featured the 7645-1 Crystal Reaper, again collecting (really exploiting and colonizing the Mars natives, but that's for another entry entirely) crystals to fuel their machinery. Therefore, it can only be assumed that these crystals, and the battle for them, were yet another in a long series of Lego themes centered around collecting crystals for energy. Aquazone premiered before elaborate backstories were established for themes (only a few years after), so this is primarily conjecture.
It's interesting that the crystal becomes such a valued Lego piece. They are chrome, which is one of the least produced Lego brick colors, and of course traditional crystals are rare and valued as well. On bricklink they average around 20 cents a piece. They really serve little purpose in building, other than being a crystal, or adding detail to something, because they can only be attached to a stud.
Back to the set however, the large glass screen would make it nearly impossible for this submarine to really be a 'deep sea predator' because the immense pressure would instantly crush the glass. The design itself is much like a shark, with a large fin on top and small fins on each side. Compared to other Aquashark sets, it's a medium sized submarine, being piloted by only one Aquashark, and seems to be built primarily for battle, but also able to collect crystals.
In closing, I believe the topic of collecting crystals will be key to many Lego themes and will be discussed in the future. Although the Aquasharks are the 'bad guys' in this theme, their connection to sharks and the sea itself makes it possible that they could be defending their world against the Aquanauts.