There is a difference. Read Craig Calfee's white paper (link below) Craig has been building carbon frames since 1987. Monocoque frames can have thin spots in some of the bends. The purpose for lugged construction is so you have uniform thickness in the tubes and they are thicker in the lugs (where most of the stresses occur).

Some may stay that Craig Calfee is biased and he might be but he build custom carbon frames and few companies can do that. He also builds a bike built for three that converts to a bike built for two, builds bikes from bamboo and repairs everyone's carbon frames.

I trust Craig's opinion on carbon frames more than anyone else.

Read his white paper:

http://www.calfeedesign.com/whitepaper1.htm