I would imagine the travel speed of a sinking aircraft fuselage would still be fairly substantial as it approached the sea-bed - because the shape of a fuselage would encourage speed through the water as it sank.
Thus there's the potential for substantial burial of at least the major portion of the fuselage, thereby making the fuselage wreckage extremely difficult to spot.
I have not seen this angle discussed anywhere in the reams of search information - but I'm guessing the ATSB is just plainly confident the tools that Fugro are using will find even a substantially-buried fuselage.
From many years experience with sonar I would suggest that if a mud is so soft that it will allow wreckage to sink in then it will also allow the search beam to penetrate and you would be very likely able to spot the signature.