I used bar end shifters for a few years during winter training, along with aero brake cables, and ran both under the bar tape for the full length of the bar. The shifter cable is stiffer and harder to bend, and was hard to tape down. I guess that the extra curves add a little to the friction factor, but I don't know because I never used them in the standard configuration. Anyhow, this was an 8 speed indexed (Shimano Dura-Ace) set up, and it worked fine 99% of the time (and the other 1% was probably because my derailleur was old and worn). The travel distance for the cables is longer, however, and you may need a tandem cable to reach the rear der.
Bob Oast
Asheville, NC