Writing a backtick (`) followed by enter produces another backtick in Sierra
A colleague of mine contacted Slack about this and their response was:


  We are aware of a related bug within Chrome and, as our newest app is closely linked with Chrome, it is unfortunately also affecting us in Slack. In this case, it's not something we can directly fix ourselves, but we've escalated it to the relevant parties.


So I guess this is not really directly linked to Sierra as is. But I'll leave the question here in case someone runs into the same problem.

And if you know a fix or a nice workaround, I'll be happy to hear it.

(So far the best I know of is pressing space after entering the backticks which isn't that bad. It still adds a key press to my usual flow but life just isn't always perfect. :) )