Yes, a few game devs will drop native Linux support because building and maintaining just the Windows version and relying on Proton will be cheaper for them. Some number of them would have inevitably dropped native Linux support anyway. Take Rocket League for example. For most games, very few would have EVER had a native version for Linux. Source: the decades of PC gaming history prior to Proton.
Even with regular WINE being available, it's not like game devs were testing how their game ran in WINE. Currently, if your game doesn't work in Proton (and therefore the Steam Deck), you get an "Unsupported" icon on your store page. Getting that Deck Verified green checkmark is an actual economic incentive for game devs to support Linux in any way, even if that way is unsavory to some.
So, like Electron, the argument is less "Electron app vs native app" and more "Electron(/Proton) app vs no app at all".
Also, given that Proton isn't preventing developers from still offering a native Linux version, you really can't say that Valve/Proton are why those devs are dropping it. The developer is still choosing to drop native support.