I'm not sure if you could do them (transfer to multiple devices) simultaneously - you might need 50 USB ports! You can, however, copy all 100 PDF files across to a single device at one time. Apologies if this explanation is beneath your level of experience.
When transferring a single PDF using the Drag & Drop method, you will notice that when you hang over iTunes a 'no entry' sign is displayed near your cursor for a short moment before the 'arrow in a box' sign indicating that the file is ready to be dropped (and copied) across to your device. When transferring multiple PDFs (say, even a few gigabytes) you must hang over iTunes for longer until your computer has done processing. Do not 'drop' them into iTunes before you see the 'arrow in a box' sign near your cursor. When you first drag them from your folder into iTunes, your PC may seem to freeze up a little. Don't worry, it is processing. As long as you keep hold of them with your mouse click over iTunes t will eventually show you the sign and you can drop them. Again, it iTunes may seem to freeze up a little whilst it is copying them across. Don't worry, give it time and it will eventually transfer the files.
Hope this is of help to at least one side of your problem. As for transferring to all 50 devices at once... perhaps that's something (if you can find enough connections) to be done from a command line.
Here are some methods that I have come across.
Consider some push method: SugarSync or dropbox addon. Depending on how often the fiels change. Most of the syncing could be done in the home office.
There are lots of ways of moving files. USB to iPad supports only "Camera" files via camera connection kit.
A simple and popular way to copy files.
Using iTures to transfer files:
Look in the app store for accessing Windows File servers.
Configure WebDave on your server.
This thread has good info.
How to transfer files from your iPad to your PC with iPad to Computer Transfer
More ways to transfer files and access Word documents:
Try the combo of:
Diskaid on your computer and FileAppPro on your iPad
Good old FTP
FileApp and FileApp Pro
I use Mac OS pureFTP server. It comes as part of PureFTPd Manager software download at this site.
---------------------- Push methods -------------------------
For syncing pc or mac folders to iPad applications.
"Using SugarSync, you simply designate folders that you want to “sync” to the cloud and it keeps everything in sync anytime you make changes. This is the way cloud storage should be done and especially if you are using your iPad for buisness or for school."
"This can be done with Dropbox as well using one of the many Dropbox addons…"
The only potential downside is that so many apps for the iPhone/iPad come with Dropbox sync built in which makes it extremely convenient.