Do they? On a board with only two M.2 slots and not much else going on that's true, but start adding additional M.2 slots and other onboard peripherals and those 16 lanes are soon going to be used up.
well ive got an MSI X570 ace, and all 3 M.2 slots on that board are populated and all run at full speed, SATA doesnt use any of the lanes as the CPU and chipset comes with controllers built in as additions, same with the USB and LAN, they have their own controllers so really you are only talking about slots that need the lanes, the only restriction with my ACE is you can only use 1 or the other PCI-e x 1 slots not both.
EDIT: Sorry only the chipset comes with a dedicated sata controller of 4 sata ports, which would explain why my ACE only has 4 any more SATA ports and you are sharing lanes, unless like you stated, it only has 2 M.2 slots.
On my ace though, im using all 3 nvme slots, 1 x 16 gpu slot and 1 x PCI x 1 slot for my sound card, finishing with 2 sata ports, im not sure if anything has been disabled as im not using anything else, but the manual doesnt say anything about loosing anything except 1 or the other x1 slot.