There are actually some rules for altitude which I applied to my players when they had access to a flying ship and had the annoying habit of flying just inside the edge of the atmosphere.
From the SRD detailing wilderness, and in particular Mountain Terrain:
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Mountain Travel
High altitude can be extremely fatiguing—or sometimes deadly—to creatures that aren’t used to it. Cold becomes extreme, and the lack of oxygen in the air can wear down even the most hardy of warriors.
Acclimated Characters
Creatures accustomed to high altitude generally fare better than lowlanders. Any creature with an Environment entry that includes mountains is considered native to the area, and acclimated to the high altitude. Characters can also acclimate themselves by living at high altitude for a month. Characters who spend more than two months away from the mountains must reacclimate themselves when they return. Undead, constructs, and other creatures that do not breathe are immune to altitude effects.
Altitude Zones
In general, mountains present three possible altitude bands: low pass, low peak/high pass, and high peak.
Low Pass (lower than 5,000 feet)
Most travel in low mountains takes place in low passes, a zone consisting largely of alpine meadows and forests. Travelers may find the going difficult (which is reflected in the movement modifiers for traveling through mountains), but the altitude itself has no game effect.
Low Peak or High Pass (5,000 to 15,000 feet)
Ascending to the highest slopes of low mountains, or most normal travel through high mountains, falls into this category. All nonacclimated creatures labor to breathe in the thin air at this altitude. Characters must succeed on a Fortitude save each hour (DC 15, +1 per previous check) or be fatigued. The fatigue ends when the character descends to an altitude with more air. Acclimated characters do not have to attempt the Fortitude save.
High Peak (more than 15,000 feet)
The highest mountains exceed 20,000 feet in height. At these elevations, creatures are subject to both high altitude fatigue (as described above) and altitude sickness, whether or not they’re acclimated to high altitudes. Altitude sickness represents long-term oxygen deprivation, and it affects mental and physical ability scores. After each 6-hour period a character spends at an altitude of over 15,000 feet, he must succeed on a Fortitude save (DC 15, +1 per previous check) or take 1 point of damage to all ability scores. Creatures acclimated to high altitude receive a +4 competence bonus on their saving throws to resist high altitude effects and altitude sickness, but eventually even seasoned mountaineers must abandon these dangerous elevations.
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So there's some rules for what happens when you travel too far up. Fort saves or be fatigued. For the dragons without cold subtypes, they should probably also have to start making fortsaves for temperature exposure at the middle range.
Also, depending on how long they travel you should factor in the fort saves and increase the difficulty across the board, considering long distance travel at high altitudes and low temperatures.
Dragons with the Air subtype should probably get a free pass on the the fortsave for high altitudes, and be treated as acclimated for all purposes.
Fire subtypes should either take a penalty or have stronger pentalites for the cold.
I would figure that Silver dragons would be handwaived on everything but the traveling forsave, since they have both Air and Cold subtypes.
Since these are all fort saves and dragons have high con, chances are they may travel higher and longer than you're wanting to and if you feel that it's too easy, add more altitude ranges or something.
Good luck, it sounds like it may be a fun adventure. What kind of dragons are they going to be anyways?
