could israel have been afraid that the fact they were killing pows been part of the cover up...a communications ship is gonna pick up the chatter on something like that....look back in the posts to the you tube...it clearly shows the murdering of the pows ..
I'm not a fan of speculating about motivation. It's too easy to start sounding conspiratorial and without information from the Israeli side about carrying out the attack, it's too easy to be wrong. The facts of the case, as they have come to light especially over the last 5 years, leave no doubt that Israel did the act and that Israel knew who and what they were attacking. That's where the focus should be until we have more information.
In researching the NSA documents, I've come across three speculations on motivation:
1) The executions occurring on the coast in the line of sight of the Liberty.
2) The impending attack on Syrian forces on the Golan Heights.
3) The attempt to bring the US into the war by sinking the Liberty and killing all hands and then blaming it on the UAR (Egypt).
Of these, I think the last is most likely. The first is an easy explanation that seems to make sense until you consider how military forces work. If it was done as a cover up of war crimes, then higher HQ would have had to know that war crimes were being committed there. A political calculation would have had to be done that it would be better to alienate the US, than have it report that war crime. Doesn't sound probable to me.
Although the Israelis were planing and executing the attack on the Golan at that time, the Liberty would have been fairly well out of position to receive useful transmissions regarding any operations against the Syrians. So, I don't think the Israelis would have thought that.
Israel was in an existential conflict in 1967. On paper, Israel was out manned and out gunned everywhere. On paper, the Arabs should have beaten the tail off Israel in 6 days instead of the other way around. The one thing the Higher HQ did know is that they were out-manned and out gunned and could really use some help. If they could have sunk the Liberty and left no, or few survivors, it would have been easy to spin this that the UAR had done it and bring the US 6th Fleet to bear on the Egyptians. This would be supported by the lack of markings on the aircraft and naval craft used in the attack. Even after the attack the members of the Liberty were not sure it was Israel. They had expected a possible attack by the UAR not Israel.
There were no Hebrew linguists on the Liberty. Anything that would have been collected by the ship that was in reference to Israeli action would have only been known when the raw data was shipped back to NSA in Ft. Meade, MD for analysis. Even then, the Liberty was focused on collecting UAR information, not Israeli information. That was their specific tasking order from NSA.