Thank you for your patience all this while. The fix of the issue is now part of InDesign’s latest update, Id 13.1
Update your InDesign through Creative Cloud app to Id 13.1
AbhinavChristine Holzmann commented
I am still having the same issue....still in InDesign 13.1 :( Scrollbar keeps disappearing on Swatches panel. Trashing prefs fixes temporarily...but I have to keep trashing them! Problem resurfaced only an hour after trashing prefs today :(Christine Holzmann commented
I am having the same issue with several panels.... Swatches Panel, Links panel and more :( Trashing prefs fixes it temporarily.