I have reproduced this issue with Cursor 2.4.28 on MacOS, with the Dark Modern color theme.
I removed items from the workbench.colorCustomizations settings, until the buttons reappeared. It was due to titleBar.activeForeground setting. The value I had (originally set by the Peacock extension) was very close to the panel’s background color. Adjusting the value to something brighter (#cccccc) displayed the button icons again.
So not a bug in Cursor; just a bad configuration.
It would be useful, however, if there were documentation somewhere explaining which settings are used by which controls; or graphically labeling the sections with their names. “activity bar”, “status bar”, “title bar”, “side bar”, and “toolbar”… it can be difficult to tell what the correct name for something is.