It depends on what chipset you use and how many extensions you use.
Also, you won't loose complete ports, but only speed. (at least on AMD chipsets)
The first thing that happens if you smash in to many extensions on a cheap chipset is, that the PCIe extension ports cut back from PCIe 3.0 to PCIe 2.0
Only if that is not enough (when even more extensions are used), it will cut back the SATA speed from 6GB/s to 3GB/s on some ports. It won't go further because the boards only have limited slots available.
that said, only a M.2 SSD and/or USB 3.1 will definitely not be enough to trigger any of that behaviour.
The X370 and B350 chipsets will most likely not have that in any situation. Only the cheap A320 and A300 chipsets might come into such situations.
The whole scenario is also true for the Intel-chipsets.