Go to the Search page (swipe all the way to the left) and search for the app name to see if it still appears and can be launched from there.
If it can, there are few things to consider.
One, if you have more than 144 apps and aren not using folders, you could have pushed the icon out of view.
If you have age limit restrictions set in Settings > General > Restrictions then apps rated over what you have set will disappear. Might not show up in the search either, come to think of it.
Check all your folders, just incase someone (or you) accidentally move it.
App icons have also been know to disappear as a glitch. Restarting or reseting the iPad will usually fix this.
If the app is on the iPad, and none of this helps, it may be necessary to delete the app and reinstall. If you are using iOS 5, you can (probably) do this in Settings > General > Usage. You can select the app under the Storage heading and delete it. If you don't have iOS 5, it will be necessary to do a complicated dance with iTunes syncing.
But before you do that, visit the App Store and make sure it still exists. You comment about it not appearing under Purchases has me worried.
To answer your questions directly, yes, Apple has the ability to pull an app off the iPad directly. (I believe Google has the same ability with the Android store) As far as I know they have never exercised this ability. It is supposed to be a last resort method to prevent the spreading of malicious or illegal apps; in which case the App Store's screening department will probably be required to fall on their swords.
Amazon exercised a similar ability with a Kindle book once. The flak they received was warning enough for just about anyone to know they better have an excellent reason to use this feature.
So the chances that Apple did this on purpose are close to nil. If they did, you'll soon hear about it all over the news; probably for the next two weeks, unless a major disaster strikes. Even then, I bet it would pull headlines for a week.