Apple developer accounts cost $100/year; if you are in the position of having more than 100 devices you need to routinely test your applications on at your large organization, you can certainly get more developer accounts (even if it is just reimbursing employees for bringing their own developer account with them as they work their job).
From what I understand, Apple's concern is circumventing the App Store, making it possible for developers to distribute apps that Apple hasn't seen yet. In short, the concern is viruses, worms and other security issues. This, I believe, is why they don't change the limits.
I'd be ok with a limit if there weren't a 1 year period for reclaiming a license. What's annoying is having a bunch of unused UDIDs - whether from departed users or abandoned phones.