Docking is preferable to depressurizing and repressurizing a shuttlebay, at least in the primitive terms of 20th century technology - so it's obvious why the "dumbed-down" technology of ST:TMP would go for docking whenever it could.
Of course, the movie also shows forcefields in action inside that shuttlebay, negating the need to pump air in or out. So the remaining reasons for not using the big bay would seem to be
1) It's still a hassle to open and close the big doors.
2) The bay has better things to do than take in a two-person taxi cab - say, loading of cargo, as seen.
3) The more docking spots the ship has, the merrier, and the two men can get closer to their destination that way.
Although curiously enough, they don't: Kirk is headed for the bridge, where there's a perfectly good docking port available, yet chooses to dock at the port the most distant from the bridge! But that probably relates to the reason why they didn't use transporters: it's more scenic that way. Kirk would miss out on the experience if arriving directly at the bridge, without going through all the sights and highlights in between.
In ST:TMP, the idea was that all shuttles could choose between going inside the mothership or just docking outside. But the shuttle type intended to be analogous to the TOS craft, the one the heroes would use for exploration, yet now featuring a docking mechanism was never included in the movie - the shuttlebay matte paintings including this design (a smaller version of Spock's courier craft) went unused. And then ST5:TFF showed that onboard shuttles still were of the same basic design as in TOS; TNG perpetuated that to the 24th century; and now the new movies demonstrate continuity of concept from the 2230s to an alternate 2260s.
Timo Saloniemi