Thought I would provide an answer to my initial question since I now have dived on the submersible DeepSee seven times in October.
1) In regard to the best time of year to go.
Clearly, I only went for one week and not throughout the year, but I did put that question to the Deepsee operators. Generally the hammerhead schools are larger and more accessible during the wet season (May through October). However this depends on the position of the thermocline, a sharp boundary between the cold deep water and the warm upper layer, set by local tides and conditions. The position generally rises in the wet season to ~40m and descends in the dry to ~100m. As the hammerheads schools stay above and near the thermocline, its position is a critical factor for scuba diving limited to 43m, but not for the submersible. However the available light for photography rapidly falls with depth, making it difficult to get good exposure much below 50m as flash is not possible through the acrylic dome. In addition, water visibility is a factor being around 18m during the wet rising to 25m in the dry. (see webpage below for graph). So the answer is not that easy, but this October there were hundreds of hammerheads per school, whale and tiger sharks, manta rays .......
2) Normally the submersible is hired by scuba divers wanting to experience a single descend to the deep at 300m, or a single shallow dive (~100m) at Everest, a rock pinnacle with a profusion of different fish, which provides fantastic panoramic photos of the passengers and a storm of small fish. But as I requested a wider experience with the sharks we followed the hammerhead schools being completely enveloped on a number of times by hundred of individuals. So the operators are thinking to expand the use of the submersible to more adventurous projects. Clearly it has the advantage of a wide range of depths, no air bubbles, extended dive times and walk on walk off and is accessible for non divers and novices, with the major downside of expense. But this is the beginning of a new era, opening a new branch of travel and exploration. As more operators come online, the expense may fall. I have noted there is another submersible (Stanleysubmarines) available to the public in Honduras, with dives to 1000ft, 1500ft and 2000ft, but I don't know more than that. I have requested details but have not yet had a reply.
3) Photographing from the submersible.
It is not possible to get to the optical centre of the acrylic dome as it is blocked by the control panel. This problem can be ameliorated by using: a small camera, a right angle viewfinder, a remote video screen with live view. Still reasonably sharp images were obtained with a full frame zoom lens up to 70mm , although the images were not as sharp as from the normal underwater housings. A +1 dioptre correcting lens did not improve the image quality. I could not find a sweet spot photographing from an arbitrary location, due to local variations in the acrylic refractive index, probably caused by stress and age.
The DeepSee has external arm, which can be used as a normal underwater housing with flash, but this is at the passenger's expense. At present only affordable by the likes of the BBC or National Geographic.
But it will come.
For those who want some additional information on what to expect, I have an illustrated article at http://www.artphototravel.net/sth-america/hammerheads-cocos-island-costa-rica/ including maps, images and short videos.