Macro Extender

I'm afraid not.

As i understand, you want do nothing when druid is in flyable area. I suggest you to rewrite macro and use internal helper function for flyable areas detection.
/cancelform [nocombat]
/run if not MEX.IsFlyableArea() then MEX:SmartMountLand() end
/cast [swimming]Aquatic Form;[combat]Travel Form;[flyable]Swift Flight Form
Don't know about API to detect swimmable area.

Macros are restricted to 255. It doesn't matter how they are created by addon code or typed by hand. Ages ago addons use some tricks to replace macros code, but now it's restricted to noncombat only, so it's totally useless.

http://my.curse.com/downloads/wow-addons/details/macroex.aspx#358946

I have a lock and paladin and Dreadsteed and Charger work as intended.
Class mounts are like all normal mounts after 3.0.2. They disappear from spellbook and moved to mounts tab.
Can you check your mounts tab?
Also (excuse me if i sound like a Blizzard support talking about "holy trinity" :D) can you disable all other addons and check again. I need to reproduce the possible bug beahvior to investigate this issue.
One more question. Does this issues start after 3.0.8?

Druid forms are something different.
I was very disappointed when Blizzard broke my universal reshifting macro in Northrend. I still can't understand how hard is to add few lines of code (i do this in ten minutes to complete Northrend flyable areas detection) and make flyable modifier to work as intended.
So i take a look for possibility to add shapeshifting to SmartMount function.
They are considered as spells and are sitll in spell book which is handled by different API unfortunately protected. So i decide don't add any frames buttons etc to keep addon simple and small in size.

This was my original idea about special handling for some classes
1. Turn On/Off Crusader aura for paladins when mount/dismount - unfortunately Blizzard put Auras on GCD.
2. Use Swift Fly Form form for druids intead of mount, use travel form when u try to mount in combat etc. Unfortunately as a i say before druid forms are protected.
3. Using Ghostwolf for Shamans
etc to make it "really smart".

AddOns are not allowed to cast spells directly without user interaction (press a key, mouse click ... ) and even CancelUnitBuff function is not protected nor limited in any way to Blizzard event restriction at all, druid forms are still protected. This is reason druids need special macro with /cancelform.
Releasing of this features requires adding some frames, button or whatever to make user interaction and allow to cast spell. If you remember pre TBC versions of Decursive with simple macro /decursive and 1 button spam, now you need to click MUF to decurse.
I was almost compete druid code in initial version, but run into restrictions issue and code was removed. You can still find player class detection, entering/leaving combat events etc, but rest is gone.

But this is really out of scope of this AddOn, it's supposed to provide only functions for macros.
Probably in the future i make some hidden button and key bind for SmartMount in anoter addon or expand this one.

MEX:Enum_Mounts() is running every time when PLAYER_LOGIN event is fired.
So if you learn a new mount it will be added to mounts table with default value from MountsNewDefaultUse.
Saved Variables are saved every time when logout or reload UI.
So if you are running addon 1st time you need to exit the game and edit saved variables file as described in ReadMe.
________________________________________________
From ReadMe.txt

* Instalation
Unzip MacroEx in your \World of Warcraft\Interface\AddOns folder and run the game.
Enter the world with all characters you want to use functions. Exit the game.
...
* Configuration
After this you will find in \World of Warcraft\WTF\Account\AccountName\RealmName\CharName\SavedVariables file named MacroEx.lua.
etc.