I had some trouble regaining root on my encrypted Nexus 5, so here is the quick guide on what finally did it.
If you do not know how to do the following or where to get the files, you might want to read up on a more comprehensive how-to first!
-> in bootloader: fastboot: flash CWM recovery (stock recovery fails file integrity in next step)
-> in recovery (sideload): adb sideload SuperSU's update.zip
CWM's default action to regain root failed, as did sideloading the update.zip via the stock recovery.
I was a little afraid I might corrupt my encrypted data partition, but so far everything looks good.