Attacks on shipping to Tobruk were carried out by Ju-87's, often escorted by Me-109F's, which were superior to every British fighter in the Western Desert. The Official History says that at times, almost every British fighter in the theater was involved in the protection of shipping.
The Axis airforces carried on harassing raids against "targets in the desert". Suez and the canal were hit by Ju-88's based in Greece. These were carried out over July to October 1941, aanmd involved 34 attacks with 300 sorties. Few of these were successfully attacked. Five were lost, of which one was in August and four were in September. This is based on the account in the Official History.