Firstly, note that players will likely be very angry if you just go about destroying or taking away stuff that their characters already have. Sundering, Disjunctioning, stealing, or otherwise removing a magic item may be understandable once in a while, but even then it will likely anger the players even if they themselves use similar tactics against enemies. An Ethereal Filcher or something might snatch up one or two items though while the PCs rest, and then make a hasty retreat into the Ethereal.
Consider that gestalts are much stronger than their ECL suggests; a 9th/9th gestalt character is at least equivalent to a 12th or 14th-level character (lack of the higher-level spells and feats means that they're not really 18th-level equivalent). So base the CR or EL of combats on the PCs being effectively 3-5 levels higher than their actual character level. Use whichever Experience and treasure scheme is worse in these cases.
Perhaps limit the treasure acquisition a bit more. Remember that many creatures, such as animals, vermin, oozes, rust monsters (especially rust monsters!!!) don't tend to have treasure, so a bunch of these thrown in once in a while will result in a slower treasure build-up. Many undead and constructs also have no treasure to loot. Dragons often have hoards of coins, and rust monsters cannot rust those, because only iron-based stuff will rust, not gold, silver, platinum, or copper coins, nor gems.
Your party does not appear to have a cleric. Undead and evil outsiders will be more challenging. Bad guys (of the right sort, anyway) can use spells or scrolls of Create Greater Undead, Planar Ally, Greater Planar Binding, and such y'know.
Throw more undead, constructs, oozes, and elementals at the party. None of these are subject to critical hits. And it's quite reasonable to assume that a great dragon will have gone to some lengths before to acquire some such minions or lair-guardians (even if the creatures are unwitting guardians). I.E. in my current Rhunaria homebrew campaign, the great wyrm gold dragon Kizaraxmallian was recently visited by the PCs. His guards included a high-level, well-equipped lizardman fighter as guardian to the entrance, a pair of cloud giants as guards to the dragon's personal chambers, a few big ol' golems as autonomous door-guards (and door-openers, for those big ol' iron doors!) to some chambers, and a few more golems in the dragon's audience chamber. The PCs, fortunately, were there on a peaceful visit. And they only saw maybe half of the dragon's underground abode; no telling what guardians might be in other corridors and chambers.
Any reasonably-aged dragon is going to have at least one, if not multiple, mid-to-high-level spellcasters serving under or alongside him/her. These spellcasters will use spells like Detect Scrying, False Vision, Arcane Eye, Augury, and the like, to foresee or deceive anyone trying to approach or spy on the lair through Scrying or whatnot. Dragons, with their great senses and blindsight, will likely use a Darkness or Deeper Darkness spell to cover their lair, or perhaps an Invisibility spell on themselves. Natural darkvision won't penetrate magical darkness, IIRC, so the dragon will have the advantage with its blindsight, whereas scryers and intruders will likely be unable to see anything through the magical darkness. A simple Fog spell will work even better sometimes. Dragons will be so intimately familiar with their lair and treasure that they won't have any trouble navigating or even fighting by blindsight alone. A dragon should be very well-prepared strategically and tactically for any battle in its lair.
I.E. in the For More Than Glory campaign that I'm substitute-DMing for a bit, the PCs attacked a juvenile (or was it young adult?) green dragon named Oruzanthanax. Their Scrying attempts saw only darkness because of the dragon's cleric minion cloaking the lair's main chambers in magical Deeper Darkness. With spells like Whispering Wind, Message, and the like, the dragon and its spellcaster minions could communicate while virtually unheard by a scryer, and the fact that the PCs didn't understand Draconic helped too. The dragon knew they were coming in this case because of a warning horn sounded by a minion outside, and the dragon had already gone out and fought them that time; both sides had to lick their wounds afterward, and in a day or two the party struck at the dragon's lair. When the PCs fought their way to the main chamber, they could only see darkness in the room, and they started spreading out to look around. Oruzanthanax emerged from the Deeper Darkness to try mauling the elven ranger, but due to the ranger's high AC and some terrible rolls on my part, the dragon was rather ineffectual at first. It used its breath weapon either right away or on the next round, I forget which, and then began chasing the ranger to try biting and mauling him.
The group finally got a concerted attack going, but Oruzanthanax continued trying to maul the ranger that had so wounded it in the previous day's battle. The party's mage Baleful Polymorphed the dragon into an iguana, but the dragon made its Will save to keep its mind and magical abilities. Then the dragon's own spellcasters emerged from the Deeper Darkness and restored their master to normal form, and then began blasting the party. Oruzanthanax mauled the mage's familiar (who had been polymorphed earlier into a hydra) and the ranger too, slaying the familiar and nearly the ranger as well. Then the party started to get the upper hand again, as more of them got in the dragon's way while the ranger backed up before launching more deadly arrow-salvos. The dragon and its kobold spellcaster minions were eventually defeated, but at least three party members were near-death, plus the mage's familiar had been slain.
I only ran that battle half-competently, on purpose, to spare the PCs mercifully from what the dragon and his two most cunning minions really could have done. And I
still nearly killed most of the party.
That is how a dragon should be run.

I could have done much nastier things with the dragon's acid, the dark cave, the minion's spells, and the dragon's tactics (I had planned such things before, but decided to go with a simpler, less deadly plan). Instead, the PCs narrowly claimed victory, patched up their wounds, hauled off the dragon's treasure hoard, and got the mage's familiar Raised from the dead.