UPDATE 3: The problem is fixed for MacOS HighSierra in MySQL Workbench 6.3.10.
UPDATE 2: It looks like the bug is recurring again in MacOS HighSierra. See https://bugs.mysql.com/bug.php?id=83658 for more details.
There is an unofficial build that fixes the problem. You can download it at: https://drive.google.com/drive/folders/0B2fTesDcrHzVRGVFWEdILWpuaEE?usp=sharing
The build was created by Bob Davenport. See https://bugs.mysql.com/bug.php?id=87714 for more details.
UPDATE: The bug is fixed in MySQL Workbench 6.3.9.
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It is a known MySQL bug: http://bugs.mysql.com/bug.php?id=83658 caused by GateKeeper Path Randomisation introduced in MacOS Sierra. See https://weblog.rogueamoeba.com/2016/06/29/sierra-and-gatekeeper-path-randomization/.
A possible workaround is to remove the Quarantine ACL:
xattr -dr com.apple.quarantine "/Applications/MySQLWorkbench.app"