Can I delete the Mobile Apps Folder from my Mac?

I would like to separate my two iPad 2 units from my desktop Mac. Each time I open iTunes it tells me how many updates to my apps are available, usually over 100. I have tons of apps stored on this system. I would rather use my iPad 2's separately and update/install apps on those individual units.
Currently, I don't connect either iPad to the computer. I did notice they were wireless syncing. I think I disabled that now. I used the option to prevent the devices from syncing automatically as well as clicking on each device and turning wireless syncing off. When I quit iTunes and then relaunch it, I'm not seeing them auto sync so I think that part may be done.
My mobile applications folder is 117.6GB in size. I would like to eventually delete that if possible. I don't particularly need the space, but I find my Mac runs much more smoothly when I get rid of excess files I don't use. Plus it saves files on my Time Machine drive that don't need to be backed up anyway. I use icloud to backup my data and iTunes Match to put my music in the cloud. I will likely leave my music on this system and then just download what music I want on each iPad from the cloud.
Are there any things I should consider while slowly separating these devices from auto syncing? It seems pointless for me to keep downloading and updating mobile apps on my desktop computer when I can't use them on it. I currently make all my purchases of apps from each individual device. Both devices are feeding from the same iTunes account/login as well. I'm thinking the only potential issue is if an app is released and then pulled from the app store. If it's pulled then the only way to recover it would be if I stored a local copy on my desktop. I don't own any tethering apps. I think I bought one app once that was a duckhunt clone that got pulled. I never play it anymore anyway. Now that I think of it, Apple's Texas Hold-Em is another but I don't use it.
Is there anything that would prevent me from doing this? Will all updates to iOS have the option of doing it on that individual unit? Will I ever need to connect them to my desktop Mac again?
Thanks!

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