Following up, almost all the problems were fixed in 2.6.19. The remaining ones appear to be these, and are now patched into the Debian package.
--- mhonarc-2.6.19.orig/lib/mhopt.pl +++ mhonarc-2.6.19/lib/mhopt.pl @@ -865,7 +865,7 @@ sub update_data_2_1_to_later { no warnings qw(deprecated); # we can preserve filter arguments - if (defined(%main::MIMEFiltersArgs)) { + if (%main::MIMEFiltersArgs) { warn qq/ preserving MIMEARGS...\n/; %readmail::MIMEFiltersArgs = %main::MIMEFiltersArgs; $IsDefault{'MIMEARGS'} = 0; --- mhonarc-2.6.19.orig/lib/mhamain.pl +++ mhonarc-2.6.19/lib/mhamain.pl @@ -1565,7 +1565,7 @@ ## sub defineIndex2MsgId { no warnings qw(deprecated); - if (!defined(%Index2MsgId)) { + unless (%Index2MsgId) { foreach (keys %MsgId) { $Index2MsgId{$MsgId{$_}} = $_; }