If I remember right, the trick with VLB and the number of slots depended on bus speed. I can't remember if the cutoff was 25/33/40, or 33/40/50, but basically, at top speed you could only run one slot reliably, but each speed grade you stepped down, you could run one more slot. The inability to run multiple VLB cards was the reason the 50 MHz 486 bus never caught on.
But there were plenty of cases that had room for both a CD-ROM drive and a 5.25" drive. And if you want SCSI, you could step up to a Pentium with PCI and drop in an Adaptec 2940 card. The last I checked on those, they were still cheap and plentiful. If that's changed, I know I have at least one I could part with.
In the 1990s, it was slightly unusual to see a system with a 3.5" floppy, 5.25" floppy and a CD-ROM drive but not unheard of. Most minitower cases could easily accomodate that many drive bays, and larger desktop systems could too. So if you can't find a system with everything you want in it, just find one with an empty bay and drop in whatever it lacks that you want.