Deep sea floors are constantly changing through subduction zones, so a not insignificant quantity of the fossilised remains will get pulled back to the upper mantle and destroyed.

Past this, one of the main ways that fossils are preserved in shallow seas are where an event occurs causing a large silt deposit on top of the dead animal, causing it to effectively be entombed in mineral deposits, which eventually leech into and replace the animals prior body structures. The faster the animal is entombed, the better preserved it will be. See the fossil that was excavated in a Canadian mine where a dinosaur with almost intact skin and innards was found. In fact the innards had not even hardened which led to the fossil breaking during excavation.

Another issue is that a lot of deep sea life is either cartilaginous or does not involve some sort of hard carapace. Bones and exoskeletons preserve better, and whilst fossil jellyfish have been found, if you weren't an expert you would think it was a smear on a rock