I suppose I should begin with the caveats that
- I do not live in Europe so I do not know how things might work there.
- I do not own or manage a business. So also clueless there.
- I have not personally ever bought anything other than free apps from the Apple App Store.
So, what I am saying is that I can not answer your question. But I also suffer from Y-chromosome induced Male Answer Syndrome, so I'll try to answer anyway.
Let's start with the assumption that Apple wants to sell you these apps. You just have to track down someone to help you either at Apple or at the company which sells this Afaria app you mentioned.
You do not mention which country in Europe you are in. But I assume there is an Apple web site either for that country or for your native language. I suggest you go to that web site and search there for information on a volume licensing program.
For example, I tried looking at http://www.apple.com/uk/ and searched for volume license.
That search turned up this link: http://www.apple.com/uk/mac/volume-licensing/
Now the page that link took me too appears to apply to volume licensing only for the OS X Lion operating system. Still, the people involved would at least know something about Apple's Volume License process. So, if you were in the UK I would suggest you contact them and start a conversation.
Even if they can't help you they could still probably point you towards other Apple people who might be able to help you.
I suggest you try something like that with the Apple web site which targets your region in Europe.
I realize this would be a tedious and frustrating process. And I hope someone else provides a better answer to your question here. But unless they do, I think your best chance of solving your problem is to start working you way through people at Apple who would want to sell you something help you.
If the apps were purchased through the Volume Purchase Program, you can install them using Apple Configurator. Add the VPP codes, connect the devices and click install. Alternatively if the apps are free you can simply drag the app into the app list and install it that way.
For more information regarding this, see this Apple KB article:
Otherwise as you mentioned the Caching Server in OS X Server would cache a copy of the app so that downloads would come from your server instead of over the internet.
Best Answer
You can't void the warranty by using non-App Store apps. The warranty covers the hardware of the device, not the OS.
Thousands, or hundreds-of-thousands, of corporate and school users develop and use apps that are not vetted through the Apple App store. In fact, Apple encourages this type of activity. Their own site for enterprise development states:
What you're told by the Apple retail employee is completely wrong.