So, the Deathwatch Rulebook has basic rules for swimming- the most important part is that there is a -30 penalty to swim in armour- and the middle adventure in The Emperor Protects had some exta rules for aquatic combat (all attack rolls have a -20 penalty, reduced to -10 if the attacker passes the Swim test).

That's all well and good for normal water, but my players are going to encounter a big, undulating ball of water (the size of a good-sized lake) held togeather only by surface tension, while hunting xenos inside a (mostly zero-gravity) space hulk. My question is: do you think the Swimming/ Aquatic Combat rules should apply here, or should I just stick with the normal Zero Gravity rules (maybe combined with a range penalty to missle weapons to represent the resistance caused by water)? I mean, it's not like they are going to be 'dragged down into the depths' by the weight of their armour…

I dunno, what do you think?

Both effects are going to be relevant - Zero-G will affect motion and balance. However while you are no longer trying to swim to support yourself in the water while its balled in zero-G the resistance to movement from the fluid IS going to have an effect on the characters.

Although you are not going to be dragged down, the way you move and the way you propel your self around in water, I would think, would be pretty much the same as in normal gravity, so a svim-test should lessen the penelty for moving and doing stuff.

Here is a pretty cool video of waves in water in no gravity:

Simple - use the Swimming skill for movement within the water, but apply any and all modifiers for moving in zero gravity. Problem solved!

I would say that it should be easier to move around, but more difficult to make actions, since the water-resistance will aid you in proppelling your self forward, but hinder, for example, swinging a sword.
For example you would make a swim-test to move around (maybe even with bonus' for the number of succes'), and a strength-test (or another appropriate test) to reduce penaltys on skill-test and other actions, such as attacking, throwing etc.