It depends on what you want to do with the bike. If you plan on doing any steep decending, or going through technical sections of trail alot, then yes, i would go with discs. V brakes are more than adequate for most cross country style riders, they have almost as much power as discs when adjusted properly. Downsides to V brakes are if you have a bent rim, your hosed, and they cannot absorb as much heat as a disc can.
Well, the nice thing about hydraulics is that they self adjust and they do have more stopping power. Mechanicals tend to go out of adjustment fairly quickly, so if you are going to be on long trails, you are either gonna have brakes that are out of adjustment near the bottom, or you are gonna be having to adjust them partway through. Also, the only decent set of mechanical disc brakes is the avid BB's. Every other mechanical disc i have seen is much more junky. You should be able to pick up a set of hayes discs for about 220 front and rear, or you can always get a used set off someone. Ebay is another good place to get them. As to your question, i would say yes, hydraulics are Definately worth the money unless you are just planning on doing skate park sessions and urban riding, where there is no prolonged use of brakes.