Flying out makes more sense, as they can then fly back in.
If they drop out, then they'd need to get in exact position under the ship, and either fly up, or be pulled up by something.
For example, here's Battleship Galactica, which has actual runways which it's fighters and other craft fly in/out of.

It also has shutes, which the vipers are fired out of. The fighters then return by landing in the runway, and are then moved back into position to be relaunched through their tubes. Bigger ships can simply take off from the runway.