I have received a reply from John Williams aviation archivist for the Margate Historical Society and he informs me that the prime suspect for the bomb crater could be the raid of 1st June 1943 which was a quick tip and run. Which was Simon's theory when Alisdair said it is a bomb crater and when I questioned what may have been the target.
John's reply is as follows;
"This may well be a left-over from the air-raid of 1st June,1943. The aircraft taking part were Focke-Wulf Fw190fighter-bombers of 11/SKG10. If it had been dropped by a Junkers Ju88 or a Heinkel He111 you would have a stick of bombs,i.e. quite a few craters in a line across the beach and lower town area.The lower part of the High Street received a 500 kg bomb from one of the twelve aircraft taking part (Messrs Tumbersand White Fuller's destroyed). The raid took place at 13.00hrs on Tuesday,1st June,1943. Bombs fell at the following locations;-St.Peter's Road, Thanet Road, Northdown Road, Laleham Road, Dalby Square, St.Mildred Road, St.Pauls Road, Milton Square, Warwick Road, Cornwall Gardens, Approach Road,High Street, Athelstone Road, Dane Park and Lower Fort Promenade. One 500kg bomb failed to explode. One bomb (500kg) destroyed Holy Trinity Church. Total casualties;-sixteen killed, thirteen seriously injured and fifty-seven slightly injured (War Graves Commission lists nine civilians dead.)."
I should also add this very same raid caused the Tudor House to list sligthly and caused the collapse of the north wall in the Grotto alter chamber. However, I am not sure the impact it had on the Margate caves.