Youve got yourself a great bike there. Dont worry about the brakes, they are very good. Only in the gloopiest mud do disk brakes have an advantage, and you tend not to go fast under those conditions.
Before you go out and abuse it, coat the clean frame with several layers of car wax, and dirt will drip off.

If you doing mixed riding, pay special attention to tyre choice.
For riding on roads, a 1.5" slick will be best.
For mixed road and trails, a touring tyre, with a solid centre bead and knobbly edges will be best.
For riding in mud, use a mud tyre rather than a dust tyre. Most bikes are sold with tyres more suited to California summertime than wet winters. Continental make some good mud tyres, with fewer knobbles, and no sharp corners for mud to hide in.
If you switch surfaces regularly, it may be worth investing in two sets of wheels, and keep them mounted with different tyres.

If you are using your bike for commuting, then I would say fit fenders. For off road use, its up to you how clean you want to stay, but dont expect a warm reception in pubs and restaurants if you are covered in mud.