The answer to the question of which is preferable, Import or Index, depends on your needs and workflows. This topic has been discussed many times on the forum, and you will find various answers. It’s not a question of right or wrong, but what works best for the user, given a set of circumstances and requirements.
Do you need to share your data with one or more other applications? Does your data come from a repository that is shared by others and may be frequently modified? If so, perhaps Index is the better capture method for you.
If not, and if you prefer DEVONthink’s environment for classifying and organizing your data, Import may be the better capture method for you.
In my case, I’m the only user of my databases. Although I often share data with others, that data is derived from my databases rather than the other way around. I’m lazy and don’t want to have to spend time on grunt work to keep my databases updated and in good shape. For me, the bottom line is that it takes less time and effort to manage a self-contained database than to manage an Indexed database.
I prefer Imported databases. I don’t have to worry whether my databases are up to date with changes in the Finder, as would be the case if they were Indexed. Nor do I have to worry about keeping the Finder updated when I create new content in a database by writing notes, adding content from a scanner or from the Web. I’m free to organize, reorganize, rename and move around content without worrying about breaking Paths, as could result in an Indexed database.
Although I use Time Machine (i’m much lazier than korm, who uses ChronoSync), my gold standard for database backup is the Database Archive, which is complete and comprehensive backup for my stand-alone databases, but would not be complete if I used Indexing (it wouldn’t contain the external files).
Most of the methods for Importing data from the Finder result in creating a copy in the DEVONthink database, leaving the original in the Finder. So we get duplication of data, that could require more storage space. My solution is simple; I delete the original files from the Finder or archive them on an external device. (One Import method, dragging folders or files in the Finder into the “Inbox” folder, actually moves the selected item(s) from the Finder into the DEVONthink Global Inbox.)
All that said about my workflows and personal preferences, I’m not fanatical about the issue. I’ve got a couple of databases that use Indexed content, because that’s useful for the purposes for which I created those databases. When working in them I accept the resulting restrictions on my freedom to move around or rename items, the additional management steps to keep them updated, and the fact that a Database Archive isn’t a sufficient backup.