Yes, the game has spaghetti code because they have spent 12 years adding features on top of features. This would happen to any and all MMOs without exception. This spaghetti code is not from 1.0 (see my signature), but from everything that came after 2.0.

The limitations seem to affect inventory and items that you can carry as well as housing. You can see an example of how a limitation was worked around by making cross-world linkshells separate from normal linkshells instead of trying to salvage them.

The game will never be free of spaghetti code but they will over time resolve old "spaghetti" issues as new ones form.