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Most of them are just variations that would be used with different display color modes, as 24-bit color displays weren't ubiquitous yet back then. There are also some icons there from later versions than 98.

I think they're 4 and 8 bit. "true colour" icons weren't available in Windows 98.

They are from earlier releases. Microsoft likes to keep old features around forever for compatibility, so 98 has icons from 95 and 95 OSR2.

To the contrary, this set includes mostly icons from 98, but there are also some from 2000/Me, plus also some icons with "cool" in their filename that I don't know where they're from. I don't think there are icons from earlier releases there.

[edit] Apparently the "cool" ones are from 98 beta builds (1351-1569) that didn't end up being ever used in actual release.

This was asked elsewhere. There's a few reasons for duplicates, like crude animations. I wrote a more detailed reply here -> https://news.ycombinator.com/item?id=39814557