Consider all the possible ways they could communicate: A patronus, an owl, or sending a messenger
Patronuses (Patroni?) JKR said in an interview that since patronuses are meant to protect you against evil things, Death Eaters never had the need to use them, which is why Snape never had to hide his from Voldy.
so . . . bye bye to that possibility
Messenger (I'm blueifying this one cause it's important): You said that they'd have to know the location of the headquarters, but you're forgetting that Voldy has his spy (at least, he thinks he has his spy
). If he wanted to send a message to the order, he would be likely to use Snape. Even though Snape can't tell anybody where the headquarters is, Voldy trust him to deliver it (again- haha!
). And Dumbledore knows that Voldy has to trust him, so he wouldn't get suspicious about how he'd get this information.
Owls: You're probably right about it being too risky, because the order could always follow the owl back. But Voldy has proved time and time again that he's too arrogant to think anyone could actually outsmart him (ooh, Volders, you're WROOOONG!

). Snape is still safer, though, so Voldemort's more likely to use owls only when he can't find Snape. It would be OK for him to use one occasionally, though.
And then there's the intercom thing . . . Well, not technically an intercom, but when I was reading the end of DH where voldy was making announcements, I couldn't help but picture an intercom system in Hogwarts, so I'm just going to call it that

. Voldy would most likely only use this for big announcements, because he likes to be dramatic sometimes.
I'd say most of what's true for Voldy's true for the rest of them.