Is he clean? I think so. Look at his career summary: excellent amateur, 3 years of nothing much at the top level in Europe 1997-1999, 6 years of winning almost everything in the USA 2000-2005, back to Europe where he performs very well and works his way back up through the ranks 2006-present. This is what a principled, strong and clean rider’s career would look like: the early failure in Europe due to being one of the few guys not on EPO, and the recent resurgence due to his being a strong rider now no-one’s on EPO.
I am reasonably certain the foregoing is what happened, and if he’s a rider who did refused to dope in the nineties when it was widely-accepted and easy to get away with; he will not have started since 2006 when it is neither widely-accepted nor easy to get away with.
The assumption that 42 is too old to be a professional cyclist may be completely out-of-date – we don’t really have any historical reference for how long a rider’s career should be if they always had good nutrition, good training & good medical support and never used amphetamines, pot belgique, EPO or inappropriate blood-transfusions. Jens Voigt is a similar age and he’s still riding with much the same style and strength that he always has had.
It’s also worthwhile to review his results from earlier this year at Tirreno-Adriatico. He finished fifth, 1:21 off the lead and 29 seconds off the podium. He and his team lost 36 seconds in the opening team time trial; if his team had performed as well as they did in the corresponding stage of the Vuelta Horner would very probably have been third in GC behind only Nibali and Froome. On the way he beat all the notable GC-contenders/climbers of the current era: Contador Velasco, Rodríguez Oliver and Kreuziger on stage 4; Froome and Nibali on stage 5. So it shouldn’t surprise anyone that he can do it again at the end of the year, particularly when he’s fresh and they are not.