I haven’t done this yet, but in MailSteward there is under Settings → Accounts the Option “…also Import email from this folder”.
Maybe you can point the folder of the DT3 Database, where your Mails are stored to this.
But be careful to leave the point below unchecked, to not delete the Mails from the DT3 Database.
That sounds very odd. DEVONthink really the cause? 90k emails not very much actually. I have much more and even when the database holding them is open, nothing happens to affect performance.