I am pretty sure Yoshida recently suggested in an interview that they were not really constrained by the spaghetti code/architecture of 1.0 anymore.
That said, spaghetti code is an issue in pretty much all development projects, to various extent. You always have some things to refactor here and there to be able to improve on it.
Sometimes you just cannot allocate resource on such work.
The whole glamour system/item database is a good example of what could probably benefit from a refactoring :P