Gosh I'm so happy to see I'm not the only one who things this is something that needs to be sorted out ^^
I'd actually love to volunteer to be a mod for this part, the problem is that I'm a bit passive in my contribution and the time I spend here atm because of school and i have no idea how long it'll take for this to clear up.
Either way i definitely support the idea.
As for the onshots that were later compiled in tankobon (and doujinshis that later got tankobon release) I suggest it is actually merged with tankobon topic. Why? Simply because in many cases it gets merged at mangaupdates as well. And may people use that to help them find stuff. And as long as you keep all the names in the topic people should be able to find it (well as long as the search works ^^; ... there is also another option though. Though I'm not sure if it'll work. When topics are moved to another section the link to it stays in the first section where it was posted. Maybe something similar could be done with topics that are merged.
Like if a topic from oneshot section is merged with topic in manga section, we have only the topic in manga section but in onshot section the topic which is actually a link to manga section topic remains. But i think that would make the sub forum look crowded.
Also as long as it's explained somewhere i don't think it should be much of a problem for members.
The bigger problem I see for the future are web manga. There may not be many of them yet but sooner or later they'll pop up. Many artist nowadays instead of releasing original doujinshis (that get picked up by a publisher later) publish web manga. Either using online stores that allow individuals to publish as well (though i guess this could be interpreted as original doujinshi), but many also offer their stuff for free on their home pages with no 3rd parties involved. I know for few artists like that since i share them sometimes, though i guess i always waited until it became some sort of "commercial" material. Not something to be worried about right now but I just wanted to point out that as long as people will feel a trace of this sort of material being welcomed here it'll increase in number as well.