When we started our work on HikaShop, Joomla 2.5 didn't exist. Joomla 1.5 was using MyISAM, so we did the same.
Why not use innoDB now ? Because it would probably require to change some of the code/queries to cope with the modification, no one expressed any problem with that choice so far, and we prefer to focus for now on fixing bugs and adding more features to HikaShop. HikaShop's architecture will evolve in the future. InnoDB might be part of that evolution, but I don't think that this is an urging topic.