I’m using version 4.3.1. I selected “Customize entry types” and checked in the drop-down menu under both Optional and Required fields but subtitle is not there. Only maintitle and mainsubtitle are…
Using version 4.3.1 on a biblatex database, the subtitle field exists for the entry type manual.
If you really need the subtitle field in a bibtex database, I see two possibilities (not tested…):
Options -> Preferences -> Define general fields (it should work in JabRef 4)
Adding manually (i.e. with a text editor, not with JabRef) the field subtitle (and its content) to your entry.