Sure, it's annoying and only really a side effect of a mute for technical reasons. But I don't see it changing, because we also want to be able to mute people who spam votes. Making two levels of mute would be over-engineering, and then you'll do "!map resign nubs" anyway, making the whole ordeal pointless.
If we only allow !y and !n it will take you a total of 5 minutes to come up with a system of communication using only that, which would be fun and all, but then why not allow people behind mute to only communicate with Morse code while we're at it. And we'd be forced to outright ban people who spam !y.
I guess the canonical answer is in the bright future with matchmaking we won't need !commands.