The walls of structure 10 inside the complex are probably the biggest ,more a case of conspicuous construction .
We know from the evidence of chambered tombs that the inhabitants were not about peace love and cuddliness , probably far from it but the "other guy " was probably your neighbour , not from the mainland of Europe or Scotland . That evidence suggests interpersonal violence not warfare ,DNA/isotope analysis might clarify that .The island(s) had a really useful defence in the surrounding seas , anyone attempting to attack them would need a fair few boats to carry the warriors across the Pentland Firth etc before even starting any attack . If thre was to be an attack and you wanted to build defences would you choose a low lying situation as at the Ness ?
And, as George has mentioned, look at Barnhouse just across the way, and Skara Brae.
The fortress thing doesn't ring true at all. I'd imagine the strip of the ness would be a terrifying place to be if under attack.
Since there was nothing as strong as cement, thinner walls would have been easy enough to breach for a persistent attacker or siege situation, unless they used massive blocks.
They seem to be suggesting the roofing was stone tiles, perhaps some were corbelled. The chamber of Maeshowe shows that making a pretty indestructible roof was not unfamiliar.
It's actually not too unlike the arrangement around cliff forts and ring forts, they had relatively small interiors with groups of undefended houses surrounding it. If you are holed up in a cliff fort or promontory fort during an attack there's not a lot of places to escape to, hence they were so heavily fortified that most opportunistic raiders would just move along. The outer ditch seems to underline a defensive role for this outer wall.
Here in Ireland we have a formidable hill fort on Baltinglass Hill that has been dated to the Neolithic. It had a strong wooden palisade and stone revetted ditches. It was burned to the ground shortly after it was built, something it has in common with many of the Bronze Age hill forts.