Thank you for your post.
I was unable to reproduce any issues with the Show/Hide Menu Bar Script Step with an Encrypted file in WebDirect with FileMaker Server 14.0.4a. In an attempt to reproduce I followed these steps:
1. Created "test.fmp12"
2. Created "HideMenu" script
show/hide menu bar script step (set to hide, lock)
3. File > File Options > Script Triggers > Set "OnFirstWindowOpen" to run "HideMenu" script
4. Encrypted file with FileMaker Pro 14.0.4 (Advanced)
5. Configured for WebDirect
6. Uploaded to FileMaker Server 14.0.4a
7. Accessed "test.fmp12" with WebDirect
-Script ran as expected.
Let me know if you have further information necessary to reproduce!