They used to make wheels with spoke nipples on the hub. For instance:
Shimano 7700 and 7800
Cane Creek

This makes for less rotational inertia, and perhaps less wind resistance. Seems to make sense to me. Why did they stop making them this way?

Made edit thanks to dabac below. Was a late night post.

I'm assuming you refer to wheels with the spoke NIPPLES at the hub?
Several options springs to mind:
-with only the "button" at the end of the spoke to transfer load, the rim needed reinforcing to hold up. Maybe This ate up most of the weight savings.
- more difficult tool access making building slower
- reduced bracing angle for (half) the DS spokes.

If the spokes screw straight into the rims, I don't see why they would need to be reinforced. It would be a smaller hole for a straight pull spoke, than for a nipple.
What do you mean by "reduced bracing angle for (half) the DS spokes". Drive side spokes? How so?
I'm willing to put up with the more difficult tool access

It is much easier to true a wheel with the nipples out at the rim. You not only have plenty of room for your spoke wrench, but you can also sense and feel your action on the rim.

John, I hear you don't like it. I've been truing wheels for 25 years. I'm willing to put up with it, for the benefits I see.

Rims are made of softer/weaker materials than spokes. A smaller hole is not a benefit, its a disadvantage. Eyeletted rims are already known to offer durability benefits over rims where the nipple goes straight into the rim. And the eyelet helps spread the load over a greater area. Something like a traditional straight-pull spoke poked straight through a rim would cause a considerable greater load concentration than even a regular nippled build. Unless the rim is reinforced at the spoke seat, I foresee regular pull-throughs.

If the DS spokes get thicker where they attach to the hub, the center line of the spokes has to be moved further away from the cassette. Even more so in a crossed pattern.
This reduces the bracing angle. Or "dish" if you prefer.

Also remember that the bicycle industry is quite influenced by fashion.
Nipples by the hub were "new" for awhile. New always sells. Then its not new anymore. Since it Didn't offer significant benefits, it was dropped. You may see it return eventually with a slightly altered sales pitch.

I was actually thinking the same thing. But it seems that rather than making it two different pieces, as in a nipple that seats into the rim, it could be designed with a gradual transition of rim material at the right heat treatment, or some localized material blend (don't ask how, I have no idea). I actually don't know how the models I've mentioned are built on the inside of the rim.

Ok, so maybe that's why on the 7801, the rim was asymmetrical, where the spokes entered to the non-DS of the rim. On the hub, they may have had to be 1.5mm further away than a spoke without a nipple.

Maybe I'm just a fan of how it looks LOL