Yes, but the stock hood does not have the side extensions like yours does. Will water get up under those and into the engine compartment?
Speaking of which, you may want to post up some pictures of the INSIDE of your hood. Does it have tubes which connect the top air vents towards the bottom of the engine compartment? Those tubes are important to keep water out. Kinda like when you hold a glass upside down in the water and the water does not flow up into the glass. There are some really smart people here that will catch stuff if you post pictures. And you don't want to fill up your engine compartment the first outing. (Like I did because I ignored my wife's question "Is this how the hood should connect?")
That link was to the 1999 Owner's Manual
BTW, the oem Yamaha Service Manual for your year Superjet is, in my opinion, a must buy. I have really found the oem Yamaha Service Manual for our '94 SN SJ to be very, very, very helpful. I don't see one on ebay for your 2001 model year right now. But snag it in the paper format when you see it come up.