A few weeks ago I went riding with a guy who has had a klx 250s for some years. (same as mine 2009 UK EFI).
He has taken the snorkel out and enlarged the hole for improved performance. He said the bike stutters for a few miles but after that the ecu adjusts itself.
I took my snorkel out. Louder and I reckon has improved grunt. Didn't notice any stuttering but mpg is down (about 10%).
Is the above right?
I ask because elsewhere have read that removing the snorkel is bad for the bike (not talking about water ingress).

 

No problem other than the noise and your aforementioned possible water issue if too deep in a stream. It will run leaner with more air available - to a point. The engine can only suck in so much air, any more opening is not needed. It is possible, but I do not know this as fact, that your EFI might have less adjustment than the injector has possible air flow. That would be a problem related to the EFI CPU.