It's a tough one C; it is quite possible, similar in fact to how the sperm whale might immobilise prey in order to catch it.
I must admit that the only cephalopod remains I have seen (from the stomach contents of sperm whales) are beaks. But from what I've read, and based on the photographs that I've seen, large squid as a rule seem to be intact, or effectively so (some without the head, others without the mantle, but without tooth marks on either end). The danger is that people are less likely to take photographs of mushed up squid from the stomachs of these things than they are to take pics of entire and very large squid, so that we get a rather biased picture of what is going on (large/intact squid might not be the norm).
The sonar/underwater detonation could have a similar effect on squid as a whale's sound emision (we call this a 'sonar canon' in the latest AFO episode. In fact we dwell on this in the latest AFO (the colossal squid/whale episode), and we also talk about frequency and squid reaction to certain frequency (ranging from attraction to alert, panic and death)). Although there's a lot of hype in the programme, there's a lot of science in there as well .... We also put a real squid in the jaws of a mechanical sperm whale and try and eat it without putting a tooth mark in it .... and it can't be done (so the whale couldn't be using the 'jaw' as a feeding aparatus; it is possibly immobilising/killing prey with the 'sonar canon' and then slurping it up. Recent evidence points to the whale actually consuming spent, dead or dying squid).
We do know that sonar has a serious effect on whales, and has been identified in a number of instances as the cause of strandings. The same could also apply to squid.
I'll keep an open mind on this NS article; he could be on to something.
IMHO it seems highly unlikely that the sonar blast on its own could cause significant organ damage - unless the poor wee beastie was investigating the air cannon at the time! As evidence, I cite the use of high volume, low frequency sound transmitted through water in order to destroy kidney stones without causing significant damage to the surrounding tissue. The machine is called a lithotripter I believe.
Perhaps they were disgorged from the stomachs of terrified sperm whales?