I'm not going to try and justify the 3K bulk limitation (though I'm also not saying it's unjustified), but I will mention some ways unlimited vaults reduce fun:
* Extra system lag from all the inventory everyone hoards: lag is not fun.
* Having 100,000 bricks in your vault breaks realism and seems too easy.
* Everybody saves every little bit of old equipment and hands it down to friends and newbies: ruins the lower end market, which is not fun for beginning crafters.
* People stockpile resources and rarely need to buy anything on the open market: reduces player interaction.
* When they collect a large load people hang on to the excess rather than selling it off: this reduces the goods on the market.
* Keeping everything means never having to decide what to keep, this reduces the challenge of the game and a certain amount of fun from choosing correctly.
There are probably other subtle ways that huge vaults hurt or help the game. But my main suspicion is that it has affected the economy and trade adversely. Now, I still feel that the builders need some relief now that the vaults have shrunk, but I think there are other ways to address that.