Horizontal and vertical distance are tracked separately
A dragon may only be able to move 200 feet horizontally through the air whilst taking a single move action, but it, like most flying creatures, can descend at any angle while moving at normal speed without even needing to make a Fly check. For example, the normal Fly rules permit the dragon to move 200 feet horizontally and 200,000 feet downward with a move action, or 200 feet horizontally and 30 feet downwards.
Since the game is generally assumed to be played in two dimensions, even when representing three dimensional combat, the rules for ascending are handled by the speed reduction instead of asking players and GMs to ascertain the diagonal vertical movement.
But you can still fall if you want
That said, should the dragon want to fall instead of just changing its height to any arbitrary lower value as a free part of horizontal movement, it certainly can do so, and regardless of the distance it falls the Fly check to negate damage remains at DC 10.
Falling doesn't actually have an explicit 500'/1000' per turn speed limit, but you can only cast spells during falls longer that, and that is the speed limit when you are falling due to weird gravity stuff:
A severe fluctuation sends the creature falling upward for 2d6 rounds, for a distance of 500 feet in the first round and 1,000 feet in each successive round.
There're also no rules, unlike for regular movement, allowing you to travel arbitrarily large vertical distances instantly at no cost while falling. Consequently, it's totally rules-legal for a GM to limit fall distance per round to 500 ft in the first round and 1000 feet per round afterwards, and indeed makes falling normally and in an unusual direction use the same rules. Another good ruling option, however, and the one I use oftest personally is to limit fall speed to 150 feet in the first round and 300 feet thereafter, bringing material plane falls in line with those under Subjective Gravity:
Under such a procedure, an individual “falls” 150 feet in the first round and 300 feet in each succeeding round.