At the same time, there are files that may look similar to each other internally but are actually used very differently practically. Consider that a program trying to inspect a CBZ (Comic Book Archive), an XPI (Firefox extension), and a JAR (Java Archive) could easily mistake each of them for a ZIP. Little surprise--all three are themselves ZIP archives with particular files within them.
How about this for a proposal: Since icons and names can't be trusted (since people may delete exposed extensions AND be suckered by hidden ones--no win here), how about color-coding the name of the program. IIRC, compressed files and folders in XP and up are shown in blue text. How about make all executable programs show up in red text, to indicate that they're executable? Now, even with extensions hidden, they're clearly visible, and the malware can't change the color of the text (since it's not subject to the program itself).