will we be holding on to motor runners helmet and other quest items forever?

Seriously

Probably, all too often this kind of thing is passed over for a fix. It was true of Oblivion, it was true of Fo3 and it will be true of F:NV.

It is a small annoying thing that your misc is made up of items you don't need or want, especially when you're wanting to sell or clear out salvage. It's hard to see and I always miss something and it's there forever. But on the bright side it doesn't weigh anything so chances are nothing will be sorted as it doesn't effect gameplay. But it would be nice if they did but not holding my breath.

Even though FO3 was a bit of a mess, I'm giving FONV the benefit of the doubt for now. The big difference for me is that Obsidian is working on this and they tend to have more follow through on their projects compared to most companies (including Beth).

Still, I wouldn't hold out too much hope for this particular fix. There's already a mod out there for that, and I would expect that Obsidian would place a higher priority on fixing the problems that modders can't (like getting stuck in the walls, weapon mods that don't work, Lucky not working in VATS, etc.).