If you’re going to use the Legacy sync, it - meaning iCloud - is going to store data on your local machine. iCloud is not under our control so there’s no guarantee of prevention.
Regarding the space used, I would disable a DEVONthink / DEVONthink To Go Legacy sync on any device.
Then on the Mac, go into System Preferences > Apple ID > iCloud and click the Manage button. Select DEVONthink To Go then click the Delete documents and data button.
This preference doesn’t give a realtime view of the deletion process, so close and return to the Manage section occasionally to check the process. Once iCloud has removed the data from Apple’s server, the DEVONthink To Go entry will disappear.
After it’s done, you could use a CloudKit sync, which syncs directly to Apple’s servers. However, in this case you should only upload one database at a time, letting it finish, then uploading the next, etc. to avoid Apple’s servers from throttling you.