Hi,
It would have been convenient on occasion to use a via to connect very sensitive RF parts of a circuit but I have always designed around it. For example it would be beneficial in one project I worked on to have a surface mount GPS antenna feed in to a module which was mounted on the other side of the board but instead I designed everything on the one side.
Presumably a via would act like an inductor (and capacitor where the boards overlap) and you would therefore require different matching components (in this case) from the aerial to the module to compensate for the inductance. Beyond that though I would expect the return loss to show a significant decrease but I cannot quantify it. Would anyone like to hazard a guess in the GPS/GSM 1500MHz+ range?
I never designed a board to test the real world effect as I always assumed it would be a poor solution. I also dont have easy access to Agilent ADS/Gensys or similar so have never 'wasted' any time on it.