It will if you don't re-tune the carbs.
The K&N filters are less restrictive than the stock airbox, and generally, your pop-off pressure will need to be lowered. If you bolt them on, without making carb changes, chances are, you will run lean, and burn a piston.
With that said... the stock airbox can flow more air than an 800 engine can use, so it's not a "Restriction" in the intake. So, putting on a set of aftermarket flame arrestors will not make anymore power on their own. Also, they provide ZERO protection from water ingestion. If you have water in the bilge, and roll the ski over... that water will go directly into the engine.
Unless you have other engine mods, and know how to tune 2-stroke engines... I recommend leaving the stock airbox on.