Bug 477787: MaraDNS 2.0 will have full IPv6 support. I have just made a beta-test release of the relevant code (MaraDNS 2.0's up-and-coming recursor, Deadwood) and encourage people to test it and report bugs on the MaraDNS mailing list.
Bug 484466: If MaraDNS is run using the duende daemonizer, sending MaraDNS a HUP signal will stop and restart MaraDNS, reloading all configuration and zone files.
Bug 486497: It's a really bad idea to bind MaraDNS to 0.0.0.0, but if you insist on doing it, it can be done if csv2_synthip_list is set.
Bug 507591: This issue was never present in MaraDNS 1.2, and has been fixed in MaraDNS 1.3.07.10 and MaraDNS 1.4.03. If Debian versions of MaraDNS still have this bug, they need to incorporate my fix, or, better yet, upgrade to 1.3.07.10 or 1.4.03.
Bug 525188: Just this last day, I have released Deadwood 2.9.01, which is the daemon that will become MaraDNS 2.0's recursive resolver. This daemon fixes a number of long-standing issues MaraDNS 1.0's recursive resolver has, including CNAMEs pointing to AAAA records.
This particular issue is one that I will not fix in MaraDNS 1.x (IPv6 does not have wide adoption yet, and MaraDNS 2.0 should be out there by the time it does), but it has already been fixed for MaraDNS 2.0.
Bug 573970: There are no plans to add this to the authoritative MaraDNS code, but the up-and-coming MaraDNS 2.0 release will use a separate daemon for recursion called Deadwood (I just released the first beta-test version of this daemon this last day), which does support "includes" via Python-compatible execfile("filename") syntax.
All other bugs appear to be Debian-specific OS issues. The next time I look at Debian bugs will probably be in a year or two.