Pen tool not drawing lines in aftereffects

What values do you have set for the Taper?
Is your layer's blending mode inadvertently set to something other than Normal?

Out of curiousity, why do you have the Shy option toggled for all your layers?

Start the troubleshooting process by creating a new comp, select the pen tool, make sure the stroke is set to a solid color and the stroke value is greater than 2 pixels, make sure Fill is off, then click and draw a simple path in the new comp. If that works then there is something wrong with the shape layer you created in the original comp. Delete it and start over. 

If the stroke does not show up press Shift + Alt/Option + Ctrl/Cmnd + k to open project settings and check the video rendering and effects settings. Try changing them. It is unlikely that the Video Preview, Display, and GPU settings in Preferences (Alt/Option + Ctrl/Cmnd + 😉 will make any difference but check them too. 

If all that fails, hold down Shift + Alt/Option + Ctrl/Cmnd the next time you start AE and delete the preferences to reset them or go to the General tab in Preferences and browse to the preferences file and rename it and restart AE. If that fails, check for updates to your build and/or reinstall.

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