See the Help > Tutorial > Scan Paper Documents.
You’re not obfuscating things in DEVONthink any more than you’re obfuscating them in the Finder. Your files aren’t stored in nice, neat little folders in the Finder despite what you think you see, but you don’t question that. It’s very simple and straightforward and essentially the same in DEVONthink. Put them in the database and if you need them elsewhere you access them in their groups no differently than in the Finder.
Syncing indexed files does not inherently consume double the disk space. This is especially true when using a remote sync option like Dropbox where DEVONthink syncs directly to their servers. For a local sync store, yes extra space would be used for the sync data.
Yes, sync includes the content of indexed files by default. This is intentional and required if you’re going to sync with DEVONthink To Go. Otherwise, there would be no contents to import on other devices. You’d end up with file placeholders and their metadata, nothing more.
There is an option to exclude indexed content when syncing (and no, it’s not a Dropbox only setting). Control-click the sync location and choose Show Info. The setting to Synchronize contents of indexed items is there but no, you should not disable it without careful consideration.
That being said, cloud services do their own file syncing, so if you index cloud-synced files, DEVONthink lets those services handle their own file management. So the files in an indexed iCloud Drive folder on Mac A and Mac B are handled by iCloud processes, not DEVONthink. Pertinent metadata about those files is synced between DEVONthink on the Macs.
But for non-cloud-synced indexed files, yes they are synced between Macs and again, yes that’s by default. Create a folder in your home directory on Mac A and index it into a database you’re syncing with Mac B. You will see the same folder in the home directory on Mac B containing the same files as DEVONthink will sync to the same relative location on each Mac.