This is based on memory. When Khan beams over the torpedoes, we are shown a shot of one of the torpedoes in its launch tube being beamed out. The schematic seen at Khan's console shows the tubes lined up on either side of what would been engineering in the TMP Enterprise
. We are shown the cryopods lying on the floor. Shuttlebay 2 is located forward of the main shuttlebay, on the port side.
Again, from memory, Scotty was not objecting to the launch tubes. I think the tubes were already in place. He was objecting to the fact that he couldn't scan the interior, and, as the torpedoes were powered by a fuel source, if these new weapons had an exotic mixture of fuel, that this mixture could be affected by the radiation, and that there might be an explosive reaction. When he asked the supply officer what was in the tubes, he was told that information was classified.