Update 06/30/2022: Lawrence Yang, Steam Deck developer, spoke to PCGAMER about the hardware change. He insisted there is no impact to performance of the different models and this change was made largely to secure the supply chain and push out more Decks. He states:

Many Steam Deck components come from multiple suppliers for improved redundancy and production capacity," Yang tells me. "One of our SSD suppliers provides PCIe Gen 3 x4 NVMe SSDs, while another provides a x2 (2 lane) SSD. 

Our team has tested both components extensively, and determined that there is no impact to performance between the two models.

Only time will now tell what the difference will actually be and how it will affect the Deck in general.

It appears that Valve has changed some of the hardware on some Steam Decks that are being released into the wild. While it isn't a major change, it is one to note as they changed this without giving notice to anyone who has ordered one.

Underneath the storage heading on the Steam Deck store page, it currently now states:

256 GB NVMe SSD (PCIe Gen 3 x4 or PCIe Gen 3 x2*)
512 GB high-speed NVMe SSD (PCIe Gen 3 x4 or PCIe Gen 3 x2*)

*Some 256GB and 512GB models ship with a PCIe Gen 3 x2 SSD. In our testing, we did not see any impact to gaming performance between x2 and x4.

It appears this decision was quietly made in late May and while Valve states that there wasn't any impact to performance while gaming, it could downgrade loading time and responsiveness. Further testing will be required to really see if the difference is noticeable.

You can check which version of the SSD you have by going into Desktop mode on your Deck. Search for "Device Viewer" and under "Devices", click the "Storage Drive" drop down. Click "Hard Disk Drive" and on the right side, it will show device information. Highlight the "Product" information and search it in google, this will show you the exact drive you have in your Deck.

Of the two Deck's in my possession, one has a Phison SSD and the other has a Kingston SSD, both are PCIE Gen 3 x4. I got the Kingston SSD one in Mid-June, so it seems that this isn't a blanket change across every 256 GB or 512 GB model. As of this writing, Valve has not responded to their reasoning behind the change, but this will be updated as soon as they do.