Well, here is the thing: They can't really take their old role as resource producers anymore. But in return, they are more powerful for the new parts of the economy that were added.
It is more like a complete shift of their use - but I don't think it made them weaker. I actually think they are more powerful AND that they work better, since they are a choice now, instead of brain dead spamming.
Also that reminds me of one more use for Habitats: They are great growth-generators for your empire, since it still is on a per-planet base, and they are far cheaper and faster to construct than Ringworlds.
You can build Hydroponic Farms on Habitats, if you really want to.