I don't think that's likely.
StatCounter uses web analytics to get those numbers. The Steam Deck probably isn't used as a web browsing device by most users. If I recall correctly, you don't even have a browser shortcut by default in gaming mode. Even if you're in desktop mode, the browsing experience is far worse than just using a smartphone. So I wouldn't think that the device is really pushing the numbers here.
GW2 is my most played game on Deck (probably around 200 hours) and I think it plays very well in most situations. The community controller layouts available via Steam work very well (full disclosure: I've created the second most popular one).
I personally would recommend playing on Deck, if you're mostly doing open world content, like leveling, world bosses, events, world completion, dailies, farming or something along those lines. Story content works very well, too.
Crafting and jumping puzzles can get a bit tedious because of the smaller screen.
WvW can work, if you're just doing some PPT.
I wouldn't recommend raiding, sPvP or intense WvW, as you'll always be limited by using a controller.
Performance-wise, the Deck holds up very well. I've set most settings to high, capped my FPS at 40 and didn't have any major issues yet.
So, all in all, I'd recommend GW2 on Deck to anyone who isn't exclusively playing very intense or competitive content. :)
Flatpacks are very restrictive by design. While this is a good thing in many cases, it makes it very difficult for tools like EmuDeck to work properly. For example, automatically installing other applications (in this case: emulators) isn‘t easily possible. This would make a flatpak version of Emudeck pretty much useless.
While I understand your concerns, I think installing an AppImage which has been built on Github from open source code just isn‘t all that risky.