Custom Thread Fields >> Custom Tables?

[ZiNgA BuRgA]

I'm not sure where you got that idea from.
The MyBB threads table isn't separated, heck the posts table isn't separated, and there'll always be a heck of a lot more posts than there ever will be threads and threadfields.
In short, number of posts >= number of threads >= number of threadfield data entries. (not all threads may have threadfield data associated with them)

If you're really keen on optimisation, I'd start with the posts table first, not the threadfields_data table.  The threadfields table only stores structural information.
Hardly an issue though, because everything is indexed appropriately.
But if you really are at the point where this additional load of accessing an index (very low additional load) is too much, you should look into MySQL table partitioning.
Separating this stuff into separate tables is simply madness from what I can tell.