It'll fit fine. Do a Google image search for "shinko 804 v-strom" and you'll find lots of photos showing entirely stock fenders and 804s.
Basically, the carcass of a knobbly tire is a wee bit smaller than other tires; the knobs don't stick out any further than a street tire.
If you plan to take a V-Strom through heavy mud with rocks, then you've taken complete leave of your senses... and yeah, you might want to raise the fender a little to stave off the inevitable disaster for a few extra feet.
2002 Suzuki DL1000 V-Strom, Dark Metallic Space Blue
1983 Suzuki GS850G, Cosmic Blue
2005 KLR685, Aztec Red - Turd II.2, the ReReTurdening