In the bad old days of J2ME at least we had rudimentary database management in the IDE, so we could clear them down before a run, for example.

I know I could write a function to empty/populate an SQLite Android db but are there any external tools I missed to help with this?

Not that this is very helpful but in the emulator you can delete an entire database in the DDMS, the database files can be found in the /data/data/ApplicationName/database (or close enough) you can of course save the database file to your pc, edit it and copy it back to the emulator, trouble is you can't do this on a device, unless there is a setting I haven't found.
Another stumbling block for me is other persistent data, I save small bits of data as preferences, I can not find any way to access then apart from programmatically.
So I tend to just remove the application when I need to clear the data out.

Seems to be crying out for a data manager tool.

Do you mean via the Preferences class? Yeah, thats really useful & I use it a lot, but the actual stored data seems to disappear into a black hole.