Frank,
I think the main reason people can be leery of mods is the fact that they are not done by the PunBB authors, and when a punbb update is released, they feel the need to wait until the mods they have installed are either tested & approved, or updated to work with the new version before they update their forum. Maybe they way mods get installed can be handled differently to help ease the pain upgrading? I know when I worked with other packages in the past, handling mods after patches and upgrades was a daunting task. You have to also remember that not everyone knows PHP & MySQL... So the easier you make a system to install and work with the better. How this is done, I don't know. I like how the plugin feature works by dropping a file with the proper name in the folder and its added to the admin section "Brilliant". maybe something like that could be done for mods except on a folder basis rather than file. I am sure most mods encompass more than one file. I believe this is how systems like post-nuke and such work.
I am relativly new to the punbb world, and I am not exactly sure how current mods are installed and handled, but I feel they should be handled as Add-Ons, and not Mods (Modifications). If a Mod has to change any of the core files or database tables to work, than IMO its not a mod in the sense of module, but rather a modification. Modules/Add-ons could be made to install their own tables, have their own functions/classes/methods if needed, and use existing functions from the core files. When looking for mods on other systems, as soon as I see that it will be modifing core files or database tables, I move on. Just my opinion. Like I said I have not had to chance to look at the MDK for mod dev guidlines so I may be all wrong in my thinking.
If the mission statement of PunBB is the embody the K.I.S.S. method, then a PM system or Poll System should not be added to the core functionality of the app itself. They can be handled as plugins - addons - modules, whatever you like to call them. I think there will be a need in the future for offical and non-offical modules. I'd feel safer installing a mod knowing that it has the blessing of Rickard.
Again, this is just my thoughts and opinions.