The Samsung Galaxy Note 9's S Pen has an integrated small battery that supplies the pen with power. If you would like to know how much battery charge the S Pen still has available, you can read this in the Android settings.
Where you can read the battery value of the S Pen is shown in this tutorial:
How full is the battery of the S Pen on the Samsung Galaxy Note 9?
1. Start from the Home screen and open the App menu
2. Go to "Settings" and then to "Advanced functions".
3. Select the entry --> S Pen and then S-Pen Remote Control
4.You now see the following overview screen
Under "Available" you will now see the battery percentage display of your S Pen.
You now know how to check on the Samsung Galaxy Note 9 how fully the battery of the S Pen is charged.