In-game, you can use any move you want (except things like Splash, that's just awful). Fake Out can be helpful on Meowstic to break Sturdy or simply get some free chip damage. I've used Fake Out in in-game teams before, and it's always worked quite well. The point of Fake Out isn't to do a ton of damage, it's a way to get a bit of chip damage and break things like Sturdy and Focus Sashes (but you won't be seeing Sashes in-game).
Use it if you want, it doesn't really matter in-game, but it can definitely be helpful at times.
Hope I helped!