Is it really so? If a player is muted, but it someone wrote in the PM, he still may answer? Why?

If it is so intended, could you make /r command as alias of /reply, not vice versa? Just because commands in this case in the plugin.yml will look better.

I agree, this seems like it is not working as intended. Just looking at the commandmsg and commandr files looks like commandr is just missing :

if (user.isMuted()) {
throw new Exception(tl("voiceSilenced"));
}

from the commandmsg file to check if a player is muted.

Disclaimer: Not a good plugin dev, just trying to help.

In my testing, issue is fixed after one of the latest dev versions with that merged PR.
#1375

This was fixed in a recent build - you can get the latest version from the build server.