I always thought that maybe Starfleet had decided that shuttles weren't necessary and that the landing bay was something that was used only ocassionally. After all, they had transporters, and could beam people or supplies anywhere they wanted. A real world analog to this is when the F4 Phantom was first put into service. It had no guns, because it had long range missiles and theoretically could shoot down any enemy from miles away and therefore there was no need for dogfighting abilities. Guess what, if you were lucky to get close enough to an F4 that its missiles were ineffective, the F4 became a very expensive sitting duck, as the military soon found out, and guns were retrofitted onto the F4. I guess the events in this episode and probably others made Starfleet realize that theory is one thing, real life scenarios another, and that it was a mistake not to have shuttles onboard.