Consider following configuration in [database] section:

    [database]
    path=mail/main

With notmuch 0.32 running:

    $ notmuch config list | grep database
    database.backup_dir=/home/miro/mail/main/.notmuch/backups
    database.hook_dir=/home/miro/mail/main/.notmuch/hooks
    database.mail_root=mail/main
    database.path=mail/main

It seem OK. Notice that backup_dir and hook_dir are absolute paths and
resolved correctly.

Running:

    $ notmuch count
    6454

All good!

Running:

    $ notmuch new
    ...
    Unexpected error with file mail/main/INBOX/cur/1615663870.253649_51.mirci,U=36739:2,S
    add_file: Something went wrong trying to read or write a file
    Error opening mail/main/INBOX/cur/1615663870.253649_51.mirci,U=36739:2,S: No such file or directory
    ...

Not good!

Setting database.path to an absolute path is a working workaround.

It seems that while notmuch can determine the correct location of the
database, when in need to access actual emails it fails. Coinciding with
the introduction of database.mail_root it seems that it's not
interpreted the same way when set (or "inherited" from database.path) as
relative value.

-- 
Miroslav Koškár
http://mkoskar.com/