No problems here, it works perfectly if the cables are cut to the right length. No one has had anything but major praise for my Mojo so far, and those that have ridden it are even more impressed.
One of the mega posters here, derby, did his own mods to route the cables on the side and under the top tube but I think the factory way is good.
It seems that Ibis were very careful about weighing the compromises necessary for any bike design and on top of making arguably the best looking bike on the market, they put a premium on accessibility (shock location), function (dw link) and serviceability (suspension components' design).
Along the top of the top tube is a very well shielded place for the cables anyway, if they wanted to hide them, I guess they could have gone internal. But internal routing might have caused maintenance complaints as well as necessitating increased development and manufacturing costs, which they'd have no choice but to pass onto us. I realize that it seems a bit odd to say that a frame for almost 2g is a good value, but in this case you definitely get what you pay for.
A few of the Ibisians are regular posters here, they might chime in on the actual reasons for that routing, I'm just guessing from having read some of their other posts and stuff on their site. Well, I guess I have the bike as reference too.
Bottom line, It works.