A recent article in the Astrophysical Journal by James Cordes, Joseph Lazio and the late Carl Sagan points out that the thin, hot gas between stars will cause radio signals to fluctuate in strength, often in only a few hours time at microwave frequencies. This could be important to SETI, because a signal that was detected one day could fade into obscurity the next. In the past, interesting signals have been checked out weeks and months after first being found. If these confirmation checks failed to find the signal, it was assumed that they were caused by interference or some other random event. There's no doubt that scintillation occurs.
Astronomers note it all the time when observing pulsars.
But it's not a real impediment to the bulk of SETI experiments being conducted today. In particular, Project Phoenix runs confirming tests on signals within minutes after first seeing them. That's quick enough that fading won't have time to set in. Project Phoenix is also being used to check out some interesting candidate signals found by Project META . Those candidates were found years ago, so the signals, if real, might be fading in and out.