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Web browsers will ask for this file a lot. Also your web server may use a considerable amount of resources just to produce a "not found error message" web page (e.g. CMS). Having said that, since the visitor would never see a "not found error message" web page for this file, web servers can run more efficiently by returning empty content by default. DreamHost adds the zero-length files in a way that won't interfere if you use your own image file instead.
There is no size limitation; however obviously if a raster image is only going to be used at a single size, ie 16x16, then it would be better to use an image specifically made for that size. Large icons will not always look good when scaled down to that size, especially anything textual. And don't forget there are 4.5 formats to choose from.
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