Yes, it would be nice to go straight up and down. Problem. And here comes the physics of it all again. All thrusters on Star Trek vessels are on the back. And impluse, warp everything goes straight behind the ship. So unless they put in an animation or design a ship to pull a Harrier you are going to have to go at an angle. Now the flip side is that there could be manuevering thrusters on all side fo the hull for docking and stuff like that but it would be ten times faster to jsut fly in a big circle then to move up at 1km/hour.
all I can say is thank god the phaser can fire straight up and in 250 degree angles so while I am moving in a circle I am still ripping the shields off my enemy.