Changing Side Panels

I'm changing the sidepanels on my 2012 Bonneville for a set of shorter ones but they do leave the air intake exposed. Is this going to be an issue or will it be OK?

 

Although not a picture of my bike these are the sidepanels I've bought from TEC.

 

I'd wondered about riding in rain but to be honest that is something I don't intend doing and as I've reached an age where the bike is unlikely to be used for more than a day trip I'm hoping I'll get away with that How do you find the breathe intake? I've been wondering about one of those and removing the air box baffling too.
I suspect they may have been looking at YR5s or YDS7s before designing these

 

I've already had the ECU altered for the loud pipes will that be OK to do the airbox mods and filter change on mine?

 

And they're on Still need to paint them though so they'll be coming off again.

 

Yeah the original owner had the dealer map it for the pipes, I have looked at the TTP map and there's no denying it looks good but funds are a bit too tight to go for it at the moment

 

They're Norman Hyde pipes.