My layout is different, but none of the experts have chimed in yet… Sorry if these ideas are very basic.
I rely on the “Dash to Panel” and “Applications menu” extensions on Gnome. In “Dash to Panel”, I have “Show Favorite Applications” checked in “Behavior”.
I am not sure what populates the top bar on your system, but the applications I have shown in my bottom one, including KeePassXC, are in “Favorites”. Are the icons there? The only other thing I would suggest is to check /usr/share/applications for the .desktop files.
I had also seen weird behavior with the Applications menu, and it apparently is still occurring, though it may not be related to your problem. When I received my system, I was not getting the icons I wanted either, and, after lots of debugging, I found a problem with the Gnome menu itself. You may want to skim that thread and look at this post. It might not hurt to try that.