SMW Bob-ombs already flash through palettes by default.
The only thing you have to do is to change color 2 in any palettes from 8-F. However, be careful, as depending on which one you want to change, it may affect other sprites. So, I suggest editing color 2 from palette F.
In other words, the circled color is the one you can change from black to something else.
As an alternative, you can recolor/edit Bob-omb's graphics, so they use more/other colors instead of black/white.