I have tracked down the Dahl quote from Going Solo:
We had nine Hurricanes at Haifa and the same number of pilots, and in the days that followed we were kept very busy. Our main job was to protect the navy ... every day they would sail up the coast past Tyre and Sidon to bombard the Vichy French forces in the mountains around the Damour river. And whenever our ships came out, the Germans came over to bomb them. They came from Rhodes, where they had built up a strong force of Junkers Ju 88s, and just about every day we met those Ju 88s over the fleet. ... then the Germans hit the destroyer Isis and we spent the whole day circling above her in relays and fighting off the Ju 88s ...
So the Ju88s were operating around Lebanon, but off the coast - they were concentrating on attacking naval units. Wikipedia notes the attack on Isis as being on 23 June, by aircraft from Lehrgeschwader 1. Dahl's book doesn't seem to say they intervened in the ground fighting - he later mentions them bombing Haifa, but this was a British-controlled port south of the fighting area.
He does not mention any escorts, and the 450 miles from Rhodes to the Lebanon coast would have been quite a long journey for most fighters in 1941 - so they were probably unescorted.
As to why they were not intercepted over Cyprus - that is unclear. It could be that the Cyprus fighters were already deployed elsewhere, that the bombers took a longer route to avoid Cyprus, or that it was simply thought to be more effective to keep the fighters over the fleet and intercept any attacks there.