Taking a peak in the game files I found these:

<IsGalacticWonder></IsGalacticWonder>

<IsPlayerWonder></IsPlayerWonder>

So they haven't totten rid of them. 

I also found this on Research Academy, but it has no value assigned.

<IsIndestructible></IsIndestructible> 

In GalCiv 2, Super Projects, Galactic Achievements, and Trade Goods, were hardcoded to be indestructible. Normal improvements, on the other hand, required the Indestructable-tag for that.

I'm wondering, if the devs just haven't gotten around to write the necessary code yet, or (if they're not going the hardcoding-route this time) if they just forgot to add the IsIndestructible-tag to all those improvements.

It's also possible, that this is intentional (because it makes it easier to test stuff, or some other reason). Still, I'm curious.