I have a MacBook Air with limited disk space as well as an iPad and an iPhone. With iCloud, do I need to keep the apps in iTunes on the MacBook anymore? When I try to delete them all in iTunes by clicking on the Apps link on the left side of iTunes and then selecting all of the apps and right clicking delete, a message appears saying that the apps will also be deleted from my iPad and iPhone. Is this really the case with iCloud or is it safe to delete them from the MacBook and free up the disk space? I think these files are stored in a folder called Mobile Applications on the MacBook.
Yes, it's safe to delete them. Just make sure you have syncing off (look for options at the bottom of your devices' summary pages in iTunes) and don't connect them to your MacBook while iTunes is open. To be safe, also go to the Apps tab (at the top, not the left) and untick Sync Applications.
But before you start deleting, in case of problems, I suggest you make sure iCloud is turned on in both your devices' settings, and perform a backup. This is all in Settings > iCloud.
As Adam has said, you should disable syncing applications and yes it is safe.
However if an app gets pulled from the App Store by Apple, which you have purchased but do not have currently install on your iOS device, you will not be able to get it back from iCloud. Whereas if you have it saved on your computer in iTunes you can get the app back by syncing.
iCloud doesn't actually back up the apps on your iPhone, it only stores your data for that app, if your restore from iCloud then it will download the apps clean from the App Store and then insert your data from iCloud, so that it appears that the entire app has been backed up.
If they backed up the entire app, for every user of an app there would be that many copies of that app on iCloud which is hugely wasteful.
So don't delete apps that are no longer on the app store else you won't be able to get them back. And if you have an app that looks like it will get pulled shortly (e.g. the app has tethering hidden inside of it) keep it on your computer. But most apps you are fine deleting and just relying on iCloud.
No, after a few years or even months you can't download your apps from the App Store (iCloud) if they decide not to sell them anymore.