when you're Company is enrolled in the Enterprise iOS Developer Programm, and you want to deploy an App in whatever way (.ips / OTA). Do all Device IDs (10000+) have to be registered and be Part of the Provisiong Profile or is it hopefully handled another way?
No you don't have to register all your devices, as specified in Apple's guide .
Just create a Distribution provisioning profile. Build your application signed with this profile with "Build and Archive" option under the Product menu.
It will open the Organizer window at the end and there you have the option to "Distribute" the app (you can choose to save the .ipa on the disk or distribute it directly).
In-house apps are not distributed through the App Store, you have several choices to deliver them to your users:
Everything is detailed here: Distributing Entreprise Apps .
For the third option, you may be interested by this software: Beta Builder .
You give it the ipa archive and the download URL, it generates deployment files.
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