Along the beastie line, you could have the traditional hunters and floaters of gas giant fauna.
Generally speaking they don't mess with ships or boats on refueling runs, too fast noisy metallic and not tasty.
However, the treasure ship in question could have become a nest. I'd use a floater form of life, partially why the ship rises and falls as different floaters grow and expand. But then there is a pack of hunters always working the nest......
If the players get past the hunters going in or out, the floaters should present a dual threat- both some sort of surprise defense, say a flamethrower instead of squid ink, and when the last floater is dead or driven off the ship starts sinking.
Other classic tropes is most targeting equipment doesn't work well in all the huge charged gas and strong magnetic field environment, specialized suits for greater pressure/poisonous atmo, and of course all those Gs for getting in, stabilize on the target, encumberance/firing problems, and getting out.
I have "greeblies" IMTU. They are the usual assortment of explosive gasbag floaters and flyers that have been like the invasive aquatic species of space. They have spread to nearly every gas giant by hitching rides on ships in the fuels scoop systems (eggs, etc..) and either thrived or couldn't make in some depending on the atmospheres.
As a result, ships almost always have what are called "bug-screens" in scoops to keep the greeblies out for various reasons. Once a really lager one got stuck in a jammed screen during a group's skim and the engineer had to suit up and go get it out. This version (there are twelve different kinds determined at random) was an armored gas bag floater with tentacles and hook-like claws. It also shot hydrogen out of it's jet siphon that would ignite and be the very flamethrower you described.
The player got the greeblie out after he inadvertently tore its sac, causing a huge jet of flame to flash out of the scoop, blasting out nearly 50 yards past the bridge's windows and the startled pilot because the gases set off more in the gas giant atmosphere. If the engineer hadn't worn his combat armor for the chore he'd have been flash-burned to ash, but as it was he got the fright of his lifetime.
None of the greeblies are intelligent, and some are friendly-ish and will float alongside a ship if you fly slowly enough, clustering around it and feeling it with their tentacles while flashing lights and colors at it. Nobody knows why, either they are trying to mate with it, worshiping the ship, or think it's just a really huge greeblie, but sightseeing ships from a planet called Kimpali will take tourists out to te gas giant there to see the greeblies up close while they swarm the craft. What with the distant lightening and occasional gasberg going by it's pretty spectacular from what I hear.
As for the ship 'sinking' I'd use that as a timer for the session. The ship is always going down, but if it were say, jammed in a frozen gasberg maybe once the players got on board and started warming up? Maybe encourage that by having the power plant operable to bring up the lights and such? Or some other reason.....anyway, have the ship lurch and make scary grinding sounds to help add tension. Figure how long it will take till they reach the point of no return, and then figure out the crisis points between then and when they board it for special events and as markers to cue sometime that will hurry them along more.
The players will try to figure out how long they have before they go own with the ship, so just tell them based on the crisis points: like...they board and the ship shortly after makes a gut-wrenching lurch as it bounces off a gasberg or is hit by lightning.
Players: Can we determine how long we have?
You: Your engineer does some calculations (roll) and he figures about an hour.
10 minutes later another bad lurch and something falls off the wreck, unleashing a flock of angry, frightened, flame-throwing floaters to attack the players....and the engineer now says you have only 15 minutes.
Then it's 10 minutes...then something happens and "could be any second, hard to know"....