--hiddenimport=_jpype is the flag for missing modules.
I’m not seeing any issues with just an import jpype (which includes loading the _jpype module).
>python -VV Python 3.11.7 (tags/v3.11.7:fa7a6f2, Dec 4 2023, 19:24:49) [MSC v.1937 64 bit (AMD64)] >python -m venv env >.\env\Scripts\activate.bat (env) >pip install jpype1 pyinstaller (env) C:\tmp\jpype-test>pip freeze altgraph==0.17.4 JPype1==1.5.0 packaging==24.0 pefile==2023.2.7 pyinstaller==6.6.0 pyinstaller-hooks-contrib==2024.6 pywin32-ctypes==0.2.2 (env) >echo import jpype; print(jpype._jpype) > test.py (env) >pyinstaller test.py (env) >.\dist\test\test.exe <module '_jpype' from '.\\dist\\test\\_internal\\_jpype.cp311-win_amd64.pyd'>