Only issue you'll probably have is if the cloud saves are for a different OS, so if you're playing on Windows make sure it's the Proton version of the game that's installed on the Deck, if you're playing a native Linux version of the game on your PC then make sure it's the native Linux version that's installed on the Deck (usual defaults to the Proton version).
It's just an issue with the cloud save feature being too dumb, the path to the save folder isn't the same on both platforms so it doesn't sync well (although I think it does on some games).
It is rare to see a game get this wrong, the last one I saw was a Borderlands. If you look at a game's Steamdb cloud listing, they list Windows's save location, and then Mac/Linux saves are expressed as a rewrite rule.
Cloud saves on PS are handled quite simply - if you didn't pay for your very own PS Plus then go fuck yourself. I have lost dozens of Aloy hours on my brother's PS4.
I've had to fuck around with my Windows saves (backed to the cloud) when installing the Linux version of Wasteland 2 and the two Pillars of Eternity games and I eventually just gave up and installed them with Proton so it would download the saves to the right place for them to work.
If you play Deadfire on multiple Linux devices you need to install with Proton compatibility otherwise cloud saves don't work at all because Steam doesn't back up the right folder (it uses the Windows folder name which has a lower case o in the word Of), that means that if you wipe your hard drive and rely on cloud saves then you're fucked because Steam will have created an empty folder to backup.
And remember, as I said, the Deck installs the Windows version by default but if you have Linux on your PC then chances are cloud saves between your Deck and PC won't work unless you force the Deck to install the Linux version of games.
As others already stated, its possible, provided the game itself is compatible with Steam Deck. While there is the Steam Cloud that saves and loads saves automatically (which does not cost you anything BTW), some games do not support the Cloud. As this is PC basically where you have access to the filesystem, you can copy files over. Only thing that is a problem is, that Steam Deck will not get recognized as a drive if you plug it to USB connection. That's a whole other story, but to answer your question, yes.