Based on dnusbaum's comment from JENKINS-34256:

A fix for this issue was just released in Pipeline: Groovy Plugin version 2.78. I think there is/was some confusion as to the expected behavior (myself included!), so let me try to clarify: When Jenkins prepares for shutdown, all running Pipelines are paused, and this is the intended behavior. The unintended behavior was that if you canceled shutdown, Pipelines remained paused. This has been fixed in 2.78; Pipelines will now resume execution if shutdown is canceled. Before 2.78, you had to manually pause and unpause each Pipeline to get it to resume execution, or restart Jenkins. Additionally, preparing Jenkins for shutdown and canceling shutdown now each cause a message to be printed to Pipeline build logs indicating that the Pipeline is being paused or resumed due to shutdown so that it is easier to understand what is happening.

Based on comments here and elsewhere, I think some users would prefer a variant of "Prepare for shutdown" in which Pipelines continue executing to completion, the same as other types of jobs like Freestyle. If that is something you want, please open a new ticket, describing your use case and the desired behavior.

[...]

If there is some other aspect of this issue that you would like to see addressed, or a different behavior you would prefer, please open a new ticket describing your particular use case.

My use case is to make restarting Jenkins master to allow upgrading Jenkins core or updating Jenkins plugins easier, because now I need to do the following:

1. wait until no pipelines are running anymore
   • which can get difficult in bigger Jenkins environments during the day i.e. normal working hours (due to steady commits triggering pipelines), but also in case there are longer lasting test suites that e.g. are triggered all around the clock
2. click "prepare for shutdown"
3. ... (continue normal work like upgrading/updating)