I don't think a lot of boards have a bunch of empty space. Some of the physical space is taken up by m.2 drives regardless of how many data lanes they use. I think to have more slots you would need an E-ATX sized board and/or one that does not have any onboard m.2.
Hi Xeromist, and thanks for your comment.
I think you are right in that mobos today have at least two M.2 sockets with heat sinks that share real estate with PCIE slots.
Latest Maximum PC (Holiday 2020) discussed the trend toward removal of 5.25" optical bays as consistent with the PC industry being driven more by gamers than by productivity workstations. Gamers don't need 5.25" bays and don't need but a few PCIE slots. They also said that modern CPUS like Ryzen generate more heat, so AIO liquid cooling is becoming more common, and they need the front panel clear to mount the radiator. I think this means we'll see fewer mobo header connectors for USB 3.0 and USB 3.1 Gen 2 cables unfortunately. I already see that happening.
Now for those wanting a lot of PCIE slots I have found a very limited number of workstation boards like this ASUS SAGE LGA2066 (Intel Skylake) that has 7 PCIE slots that can be configured as four X16, or as one X16 plus six X8. That's 64 PCIE lanes on the slots. It can also mount two M.2 NVME drives.
The form factor for the SAGE is SSI CEB, which according to Wikipedia is "Created by the Server System Infrastructure (SSI) forum. Derived from the EEB and ATX specifications. This means that SSI CEB motherboards have the same mounting holes and the same IO connector area as ATX motherboards."
Funny thing, the E-ATX boards are size 305 x 330 mm while the CEB board is 305 x 267 mm yet it's the CEB that has lots of PCIE slots.
I have not found a comparable workstation board for Ryzen or Threadripper.