What makes Devonthink not being able to import all emails from Apple Mail ?
A couple of things spring to mind: An E-Mail with the same ID has already been imported and is contained somewhere within the database (including trash); the E-Mail hasn’t been (completely) downloaded to Mail; any other reason possibly detailed in the log?
What @Blanc mentioned is the first thing to consider / look at.
If you are copying emails into other mailboxes in Apple Mail, the copies won’t be imported.
However, if you enable DEVONthink’s Preferences > Fies > Emails > Messages: Previously imported will become replicants, the copies in the other mailboxes will be imported but as replicants.
Do you import the emails via View > Sidebar > Import? This interface skips also spam by default, see options on the right side.