Is a 4090 practically better than a 3090? I just built a new home DL PC with two 3090s because I knew I could fit them both in the case, whereas with the 4090 it seems more than one could be difficult. Also wondering if I can pool the RAM somehow, nvlink won't work because the 3090s are different sizes, and apparently nvlink doesn't do much more than pcie anyway.
Basically 'it depends' is the answer to all your questions, but dual 3090s is a perfectly fine choice. Though ideally you would have NVLINK since it is an advantage over the 4090. In some specialized situations it is possible to have NVLINK act a lot like 48GB of memory, but if you don't already know if you can leverage NVLINK, you very likely aren't in that situation.
tangential but the size of 4090 seems to be a mistake and hindering usecases like this. I believe NVIDIA changed to the samsung process a bit late and it produces less heat, but they have communicated to OEMs about the cooling requirements so nobody wants to redesign their card. I expect some aftermarket brands to create "slimmer" 4090 coolers to enable aircooled dense 4090 workstations.
Gigabyte produced a dual slot 3090 for a little while before Nvidia pressured them to discontinue production[0].
I suppose we might see "slimmer" 4090s at some point but even if the design is (somehow) possible it's clear Nvidia won't allow their partners to manufacture dual slot versions of RTX cards that could possibly compete with higher end cards.
