Clark crashed into the woods at Hockenheim running in the rain. The lack of track safety barriers was common then and we can blame part of it on the track itself. He was an excellent wet driver, but in those conditions anything can happen.
Colin Chapman was beginning to ride high with his company and it was generally acknowledged that Lotus was always a bit ahead of the curve on many things, including using lighter materials when the technology wasn't really there yet. Whether a rear suspension component broke or there was a tire problem still falls under speculation. Knowing Chapman's proclivity for using questionable, lightweight, parts, the rumor mill was always bent toward the car having a problem. Also remember that Colin was less than loved by many. The other thing is that this was a Formula 2 carwhere more testing went on especially as the F1 standards were about to change so the F2 program was important.
Then there was Jimmy Clark himself. While most from Moss to Gurney to Stewart and the majority of the racing world acknowledged him to be one of the best that ever slid into a cockpit, he had one great failing according to some drivers including Jack Brabham. Jimmy knew little about the cars themselves in terms of engineering. He could communicate problems in setup quite well but relied on others to be sure the bits were all stuck together. To a man like Brabham (and later also remarked upon by the great Mark Donahue) this was taking an ultimate risk that could have been avoided. Interestingly enough, Mark Donahue, without question the finest engineer and mechanic to ever drive (and drive superbly), was killed due to a mechanical failure.
Who knows really Jon? As the saying goes, "That's racin'."