I also have this issue using Sonoma 14.6.1 and Obsidian 1.6.7 (installer 1.4.13). It doesn’t seem to occur in the sandbox vault, so I moved all my files to a new vault with all the plugins turned off, then I incrementally turned on plugins and checked to see if the problem reappeared. It did not for any one plugin, but it does still occasionally appear for no reason that I’ve been able to figure out. Restarting Obsidian often fixes the issue, but only temporarily.
I recently started using Notion again after about a year of avoidance. It appears to have a similar issue, where attempts to click certain menus–those in the top, right-hand corner–is difficult. Clicking the very bottom of the menu icons works every time, but the top ~3/4 of the icons just briefly changes my mouse pointer, but it does not open the menus. The same is true of Obsidian’s tabs: clicking the bottom ~1/4 of the tab works every time, but anything above that just causes my pointer to change. Strangely, Notion’s tabs do not appear to be affected.
I mention the issue with Notion because I believe both Notion and Obsidian are Electron apps, which might be relevant. Maybe there’s some toolkit used for certain interactive elements that is interacting with Mac’s menu bar in unexpected ways? The menu bar isn’t visible in fullscreen mode, but maybe the OS still reserves that space in some way that conflicts with certain Electron elements. Just spitballing.