Can I transfer 100 PDFs files from Windows to Acrobat Reader on iPad without going through iTunes or transferring the file one by one?
Provided you have space on your iCloud Drive, you could upload files via a browser on Windows to iCloud, then download those files/folder to your iPad using the "more locations" function in Adobe Acrobat Reader.
Other services like Dropbox, OneDrive, and Google Drive should be supported as other locations in the file browser.
If you want to copy these files from the Files app (from iCloud Drive, Dropbox, Google, etc.), you can navigate to the files, tap "Select", then tap the files you wish to transfer. Tap the folder icon at the bottom of the screen. Then select the path you wish to copy files to, which is On My iPad > Adobe Acrobat, then tap Copy. Do note that these files are copies and are not the originals. Any changes or notes you make on the copied files will only exist on your device and not on the cloud.
These screenshots show a basic outline of the instructions above.