I've used my 250ES many times on trails with deep water..the usual protocol is stay on the gas and lean back enough to let the natural front bouyancy do the work. The steering neck stays out of the water and she can breathe!!
Usually up to 3ft of water before things get dicey.
The issue with snorkling a BR is a matter of geography..by that I mean, where to run the pipes?
I've seen guys plumb them from the box, along the tank side forward and up. A terrible idea..both due to the fact it restricts your arm on the handlebars and 2nd because you'll eat PVC if you wreck.
The second way is to run it back, which means cutting your trunk box since there's just no damned room under the back to run it.
I'd suggest leave it as is and practice your skills..once you get the feel for it you'll be fine.
Current toys..
1986 Honda 350X..trail bomb!
1985 Honda 250SX..my main mudder
1985 Honda 250ES..Back in Black Trike
Current non-trike toys:
1990 Honda TRX300FW
1995 Seadoo GTX
1998 Polaris Indy Lite 340(Nearly new looking)
1998 Polaris Touring 500
1998 Club Car (electric)