Maybe I'm just showing my age here, but a hand-built Windows machine without drive bays just seems odd to me. And I've noticed, too, that the number of PCI-E slots on motherboards is dropping. The modern enthusiast machine seems to be a giant PCI-E GPU, possibly even mounted sideways, some very funky cooling solutions, and NVMe SSDs.
(... then again, if motherboards still had floppy controllers, my main Windows machine probably still would have one of those lovely 3.5" Mitsumi combo card reader/floppy drive things. It's a Windows machine with a giant case, not 12-inch MacBook, what's the downside to keeping another drive type or two around?)
There's still a plethora of motherboards out there with multiple PCI-E slots. Most have two long (x16/x8) slots and 2-3 x1 slots. As far as drive bays go, these motherboards also have multiple M.2 slots, and the cases themselves usually have SSD mounts on the backside of the motherboard tray. The only time you really see the number of PCI-E slots dropping is when you're looking at smaller form factor motherboards that simply do not have the room for more than the one x16 slot.
I have two custom built PCs right now - one for gaming, the other as a media server and smart home control hub. Both of them support a minimum of two M.2 drives onboard, and have a total of five PCI-E slots. Both cases also have a cage for dual HDDs, which are hidden from sight at the bottom of the case. Neither case has bays for optical drives, but when was the last time anyone truly needed one of those?