Can many iPads have a “master” Apple ID and a second, “personal” Apple ID

There is no limit and having more is not necessarily better. Having all your devices registered under one Apple ID has the benefit of having all your purchases pushed to them without having to manage multiple accounts. So your wife can enjoy an app on her iPhone 4 just the same as you can enjoy the same app on your iPad 2, without needing to purchase the app a second time (once for each device), or constantly logging in and out of various Apple IDs to install and update.

I find it is always better to pool your purchases to one account and register your devices under that single account. Having multiple Apple IDs requires that one micro-manage each account (iTunes will only check for updates for the current Apple ID), which can be bothersome at the best of times and a nightmare at the worst of times.

One advantage of having separate Apple IDs, however, is that each account belongs to its respective owner and can be registered to their own payment methods. But if you share your finances, that is of little value to you.

iCloud is bound to its respective Apple ID, so if you have just the one, all the features of iCloud would permeate through any device registered to that account. That means if you downloaded an app on your iPad 2, it would appear on your wife's iPhone 4. You would also share documents, pictures, music, etc. (anything supported by iCloud and expressly enabled by you) across all your devices as well—email as well. iCloud would essentially unify them and their content.

Multiple Apple IDs are not required. You may also find this article on managing multiple devices (although somewhat dated when iCloud launches).

I don't think there is any enforced limit for using one account on lots of devices if all you care to do is use Find My Phone. You will run into the 10 device limit if you try to install apps using this ID, but just entering it into iCloud and only turning on FMP (FMi / FMiP ??!) should scale past the limits people normally reach when using one ID for multiple devices.

Even if you get away with this, your users might get confused or wish to use Find My.../iCloud themselves and find you have locked their device

You might want to reach out to your Apple account rep to avoid running into several anti-fraud efforts that prevent this sort of mass scale deployment if you try to use one Apple ID for say the App Store on so many devices. In addition to that specifically being against the licensing terms, you will face delays if and when this account gets locked, so plan to test things out with a small group (say 3-8 devices sharing one ID) as a pilot before you decide how to manage all 100 devices.

There are quite a few MDM packages available, but without knowing your specific situation, it will be hard for you to determine if automating some of the management will be a good investment or if you can just use the Apple Configurator to set up your deices and depend on the end users to manage their Apple ID/iCloud accounts and not mess with your one set up to track all the devices.